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USGS2020

Seasonal variation in sediment delivery across the bay-marsh interface of an estuarine salt marsh

Sediment transport across bay–marsh interfaces depends on wave energy, vegetation, and marsh-edge morphology, and varies over a range of timescales. We investigated these dynamics in a tidal salt marsh with a gently-sloped, vegetated edge adjacent to northern San Francisco Bay. Spartina foliosa (cordgrass) inhabits the lower marsh and Salicornia paciﬁca (pickleweed) predominates on the marsh plain. We measured suspended-sediment concentration (SSC) and hydrodynamics in bay shallows and along a 100-m cross-shore transect in the marsh, during winter and summer. Four-year averaged accretion measured with marker-horizon plots was twice as great along the marsh transect as adjacent to a tidal creek, 50 m from the bay. We estimated deposition and trapping eﬃciency from the time-series data to assess its variation with season and wave energy. At high tide the transition zone (between cordgrass and pickleweed) was usually erosional, the pickleweed zone was depositional, and both erosion and deposition increased with wave energy, as did the landward position of maximum deposition. Erosion from the transition zone accounted for approximately one-third of the sediment ﬂux into the pickleweed. In the pickleweed zone, SSC, the diﬀerence between ﬂood- and ebb-tide SSC and trapping eﬃciency were greater in summer than winter for comparable wave conditions, which we attribute to increased sediment trapping by dense summer cordgrass. Moderate waves in summer (46%) accounted for more annual accretion in the pickleweed zone than larger waves in winter (28%), although the contribution of winter storms was diminished by the dry winter during the study.

California↗

USGS2016

Observations of wave transformation over a fringing coral reef and the importance of low-frequency waves and offshore water levels to runup, overwash, and coastal flooding

Many low-lying tropical islands are susceptible to sea level rise and often subjected to overwash and flooding during large wave events. To quantify wave dynamics and wave-driven water levels on fringing coral reefs, a 5 month deployment of wave gauges and a current meter was conducted across two shore-normal transects on Roi-Namur Island in the Republic of the Marshall Islands. These observations captured two large wave events that had waves with maximum heights greater than 6 m with peak periods of 16 s over the fore reef. The larger event coincided with a peak spring tide, leading to energetic, highly skewed infragravity (0.04–0.004 Hz) and very low frequency (0.004–0.001 Hz) waves at the shoreline, which reached heights of 1.0 and 0.7 m, respectively. Water surface elevations, combined with wave runup, reached 3.7 m above the reef bed at the innermost reef flat adjacent to the toe of the beach, resulting in flooding of inland areas. This overwash occurred during a 3 h time window that coincided with high tide and maximum low-frequency reef flat wave heights. The relatively low-relief characteristics of this narrow reef flat may further drive shoreline amplification of low-frequency waves due to resonance modes. These results (1) demonstrate how the coupling of high offshore water levels with low-frequency reef flat wave energetics can lead to large impacts along fringing reef-lined shorelines, such as island overwash, and (2) lend support to the hypothesis that predicted higher sea levels will lead to more frequent occurrences of these extreme events, negatively impacting coastal resources and infrastructure.

Journal of Geophysical Research C: Oceans↗

USGS2014

Simulation of the effects of rainfall and groundwater use on historical lake water levels, groundwater levels, and spring flows in central Florida

The urbanization of central Florida has progressed substantially in recent decades, and the total population in Lake, Orange, Osceola, Polk, and Seminole Counties more than quadrupled from 1960 to 2010. The Floridan aquifer system is the primary source of water for potable, industrial, and agricultural purposes in central Florida. Despite increases in groundwater withdrawals to meet the demand of population growth, recharge derived by infiltration of rainfall in the well-drained karst terrain of central Florida is the largest component of the long-term water balance of the Floridan aquifer system. To complement existing physics-based groundwater flow models, artificial neural networks and other data-mining techniques were used to simulate historical lake water level, groundwater level, and spring flow at sites throughout the area. Historical data were examined using descriptive statistics, cluster analysis, and other exploratory analysis techniques to assess their suitability for more intensive data-mining analysis. Linear trend analyses of meteorological data collected by the National Oceanic and Atmospheric Administration at 21 sites indicate 67 percent of sites exhibited upward trends in air temperature over at least a 45-year period of record, whereas 76 percent exhibited downward trends in rainfall over at least a 95-year period of record. Likewise, linear trend analyses of hydrologic response data, which have varied periods of record ranging in length from 10 to 79 years, indicate that water levels in lakes (307 sites) were about evenly split between upward and downward trends, whereas water levels in 69 percent of wells (out of 455 sites) and flows in 68 percent of springs (out of 19 sites) exhibited downward trends. Total groundwater use in the study area increased from about 250 million gallons per day (Mgal/d) in 1958 to about 590 Mgal/d in 1980 and remained relatively stable from 1981 to 2008, with a minimum of 559 Mgal/d in 1994 and a maximum of 773 Mgal/d in 2000. The change in groundwater-use trend in the early 1980s and the following period of relatively slight trend is attributable to the concomitant effects of increasing public-supply withdrawals and decreasing use of water by the phosphate industry and agriculture. On the basis of available historical data and exploratory analyses, empirical lake water-level, groundwater-level, and spring-flow models were developed for 22 lakes, 23 wells, and 6 springs. Input time series consisting of various frequencies and frequency-band components of daily rainfall (1942 to 2008) and monthly total groundwater use (1957 to 2008) resulted in hybrid signal-decomposition artificial neural network models. The final models explained much of the variability in observed hydrologic data, with 43 of the 51 sites having coefficients of determination exceeding 0.6, and the models matched the magnitude of the observed data reasonably well, such that models for 32 of the 51 sites had root-mean-square errors less than 10 percent of the measured range of the data. The Central Florida Artificial Neural Network Decision Support System was developed to integrate historical databases and the 102 site-specific artificial neural network models, model controls, and model output into a spreadsheet application with a graphical user interface that allows the user to simulate scenarios of interest. Overall, the data-mining analyses indicate that the Floridan aquifer system in central Florida is a highly conductive, dynamic, open system that is strongly influenced by external forcing. The most important external forcing appears to be rainfall, which explains much of the multiyear cyclic variability and long-term downward trends observed in lake water levels, groundwater levels, and spring flows. For most sites, groundwater use explains less of the observed variability in water levels and flows than rainfall. Relative groundwater-use impacts are greater during droughts, however, and long-term trends in water levels and flows were identified that are consistent with historical groundwater-use patterns. The sensitivity of the hydrologic system to rainfall is expected, owing to the well-drained karst terrain and relatively thin confinement of the Floridan aquifer system in much of central Florida. These characteristics facilitate the relatively rapid transmission of infiltrating water from rainfall to the water table and contribute to downward leakage of water to the Floridan aquifer system. The areally distributed nature of rainfall, as opposed to the site-specific nature of groundwater use, and the generally high transmissivity and low storativity properties of the semiconfined Floridan aquifer system contribute to the prevalence of water-level and flow patterns that mimic rainfall patterns. In general, the data-mining analyses demonstrate that the hydrologic system in central Florida is affected by groundwater use differently during wet periods, when little or no system storage is available (high water levels), compared to dry periods, when there is excess system storage (low water levels). Thus, by driving the overall behavior of the system, rainfall indirectly influences the degree to which groundwater use will effect persistent trends in water levels and flows, with groundwater-use impacts more prevalent during periods of low water levels and spring flows caused by low rainfall and less prevalent during periods of high water levels and spring flows caused by high rainfall. Differences in the magnitudes of rainfall and groundwater use during wet and dry periods also are important determinants of hydrologic response. An important implication of the data-mining analyses is that rainfall variability at subannual to multidecadal timescales must be considered in combination with groundwater use to provide robust system-response predictions that enhance sustainable resource management in an open karst aquifer system. The data-driven approach was limited, however, by the confounding effects of correlation between rainfall and groundwater use, the quality and completeness of the historical databases, and the spatial variations in groundwater use. The data-mining analyses indicate that available historical data when used alone do not contain sufficient information to definitively quantify the related individual effects of rainfall and groundwater use on hydrologic response. The knowledge gained from data-driven modeling and the results from physics-based modeling, when compared and used in combination, can yield a more comprehensive assessment and a more robust understanding of the hydrologic system than either of the approaches used separately.

Florida↗

USGS2010

Wind-enhanced resuspension in the shallow waters of South San Francisco Bay: Mechanisms and potential implications for cohesive sediment transport

We investigated the driving forces of sediment dynamics at the shoals in South San Francisco Bay. Two stations were deployed along a line perpendicular to a 14 m deep channel, 1000 and 2000 m from the middle of the channel. Station depths were 2.59 and 2.19 m below mean lower low water, respectively. We used acoustic Doppler velocimeters for the simultaneous determination of current velocities, turbulence, sediment concentration and fluxes. Maximum current shear velocities were 0.015 m s −1 at the station further from the channel (closer to the shore) and 0.02 m s −1 at the station closer to the channel. Peak wave-induced shear velocities exceeded 0.015 m s −1 at both stations. Maximum sediment concentrations were around 30 g m −3 during calm periods (root mean square wave height <0.15 m). During wavy periods, sediment concentrations increased to 100 g m −3 and sediment fluxes were 5 times higher than in calm conditions (0.02 g m −2 s −1 versus >0.10 g m −2 s −1 ) at the station further from the channel 0.36 m above the bed. Closer to the channel, sediment concentrations and vertical fluxes due to wind wave resuspension were persistently lower (maximum concentrations around 50 g m −3 and maximum fluxes around 0.04 g m −2 s −1 ). Most resuspension events occurred during flood tides that followed wave events during low water. Although wave motions are able to resuspend sediment into the wave boundary layer at low tide, the observed large increases in sediment fluxes are due to the nonlinear interaction of wind waves and the tidal currents.

California↗

USGS2000

Debris flow monitoring in the Acquabona watershed on the Dolomites (Italian Alps)

In 1997 a field monitoring system was installed in Acquabona Creek in the Dolomites (Eastern Italian Alps) to observe the hydrologic conditions for debris flow occurrence and some dynamic properties of debris flow. The monitoring system consists of three remote stations: an upper one located at the head of a deeply-incised channel and two others located downstream. The system is equipped with sensors for measuring rainfall, pore pressures in the mobile channel bottom, ground vibrations, debris flow depth, total normal stress and fluid pore-pressure at the base of the flow. Two video cameras record events at the upper channel station and one video is installed at the lowermost station. During summer 1998, three debris flows (volumes from less than 1000 m 3 up to 9000 m 3 ) occurred at Acquabona. The following results were obtained from a preliminary analysis of the data: 1) All of the flows were triggered by rainfalls of less than 1 hour duration, with peak rainfall intensities ranging from 4.8 to 14.7 mm / 10 minute. 2) Debris flows initiated in several reaches of the channel, including the head of the talus slope. 3) The initial surges of the mature flows had a higher solid concentration and a lower velocity (up to 4 m/s) than succeeding, more dilute surges (more than 7 m/s). 4) Total normal stress and pore fluid pressures measured at the base of the flow. (mean depth about 1.1 m) were similar (about 15 kPa), indicating a completely liquefied flow. 5) Peak flows entrained debris at a rate of about 6 m 3/m of channel length and channel bed scouring was proportional to the local slope gradient and was still evident in the lower channel where the slope was 7°.

Acquabona Creek, Alps, Boite River, Dolomites↗

USGS2021

A numerical study of wave-driven mean flows and setup dynamics at a coral reef-lagoon system

Two-dimensional mean wave-driven flow and setup dynamics were investigated at a reef-lagoon system at Ningaloo Reef, Western Australia, using the numerical wave-flow model, SWASH. Phase-resolved numerical simulations of the wave and flow fields, validated with highly detailed field observations (including >10 sensors through the energetic surf zone), were used to quantify the main mechanisms that govern the mean momentum balances and resulting mean current and setup patterns, with particular attention to the role of nonlinear wave shapes. Momentum balances from the phase-resolved model indicated that onshore flows near the reef crest were primarily driven by the wave force (dominated by radiation stress gradients) due to intense breaking, whereas the flow over the reef flat and inside the lagoon and channels was primarily driven by a pressure gradient. Wave setup inside the lagoon was primarily controlled by the wave force and bottom stress. The bottom stress reduced the setup on the reef flat and inside the lagoon. Excluding the bottom stress contribution in the setup balance resulted in an over prediction of the wave-setup inside the lagoon by up to 200–370%. The bottom stress was found to be caused by the combined presence of onshore directed wave-driven currents and (nonlinear) waves. Exclusion of the bottom stress contribution from nonlinear wave shapes led to an over prediction of the setup inside the lagoon by approximately 20–40%. The inclusion of the nonlinear wave shape contribution to the bottom stress term was found to be particularly relevant in reef regions that experience a net onshore mass flux over the reef crest.

Journal of Geophysical Research-Oceans↗

USGS1999

Sora rail studies on the Patuxent River, Maryland

The freshwater marshes of the tidal Patuxent River are well known for their annual fall concentration of migrant soras ( Porzana carolina ) and were formerly the most famous rail hunting grounds in the Chesapeake Bay region. Because of concern over the apparent long-term decline in number of soras and the decline in the quality of the Patuxent marshes, especially the loss of wild rice ( Zizania aquatica ), the Maryland National-Capital Park and Planning Commission (MNCPPC), co-steward of the Jug Bay National Estuarine Research Reserve, sponsored rail-related research beginning in 1987. Past efforts focused on developing efficient trapping techniques, age and sex criteria, and monitoring body mass dynamics. Noted progress was made in developing digital playback systems and trap improvements to enhance sora captures. These improvements increased capture success by over an order of magnitude and resulted in capture of 2,315 soras and 276 Virginia rails ( Rallus limicola ) in the 5 year period, 1993-97. Although these methods demonstrate the efficacy of banding large numbers of soras on migration and possibly winter concentration areas, captures at the Patuxent River site have been 70-90% hatching-year birds and recoveries and recaptures have been virtually nonexistent. With the present effort, this outcome precludes population parameter estimation using traditional capture-recapture or recovery model methodologies. In 1996, studies were initiated to employ radio telemetry methods to investigate length of stay, habitat use, survival, and migration characteristics of fall migrant soras. These studies are ongoing and will be continued through 1998 with a grant from the U.S. Fish and Wildlife Service's Webless Migratory Game Bird Research Program and support from the U.S. Geological Survey's Patuxent Wildlife Research Center. Supplemental funding has also been provided by MNCPPC, FWS Region 5, the Maryland Ornithological Society, Quail Unlimited, and Prince Georges Community College. During 1996-97 we developed a successful radio transmitter attachment technique to secure 1.8g radio transmitters over the synsacrum of migrant soras. We modified Rappole and Tipton's (1991) leg-loop attachment method by addition of a waist loop to prevent soras from slipping transmitters over their short tails. Thin gauge (0.6 mm) elastic thread proved ideal for attachment and allowed for girth expansion associated with fattening during stopover. Sixty instrumented soras have been monitored in two years of study from early September until early November. Only a single mortality was recorded and 41 (68%) were confIrmed and another 13 (total 90%) were believed to have migrated from the study area. Only a single bird slipped a radio transmitter. Most birds demonstrated a sedentary nature in the marsh throughout stopover. Average length of stay was 44 days in 1997 (n=29) with peak departure occurring 20-24 October. Departing migrants were detected using a receiver/data-logger monitoring system placed 4 miles down river from the study site. Thirty-six of 37 (97%) soras departed in a 2-hour window of time, beginning 1 hour after sunset. Departure was synchronized with cold fronts on clear, starlit nights. Twenty-five soras were monitored on migration from 8 km to as far away as 770 km. Findings indicate migration flight speeds of 40 to 50 mph and a direct southward orientation from the study site at least until contact with the Atlantic Ocean west of Cape Lookout, North Carolina. We also attempted to monitor passage of migrant soras radio tagged at Iroquois National Wildlife Refuge in western New York by biologist Soch Lor. None were recorded passing a monitoring unit at Haldeman Island in the middle of the Susquehanna River 10 miles north of Harrisburg, Pennsylvania. This further corroborates our findings that when migrating overland, soras move in a direct southward orientation and are not following land features such as major rivers

Book chapter↗

USGS2016

The Outer Banks of North Carolina

The Outer Banks of North Carolina are excellent examples of the nearly 300 barrier islands rimming the Atlantic and Gulf coasts of the United States. These low, sandy islands are among the most dynamic natural landscapes occupied by man. Beach sands move offshore, onshore, and along the shore in the direction of the prevailing longshore currents. In this way, sandy coasts continuously adjust to different tide, wave, and current conditions and to rising sea level that causes the islands to migrate landward. Despite such changes, barrier islands are of considerable environmental importance. The Outer Banks are home to diverse natural ecosystems that are adapted to the harsh coastal environment. Native species tend to be robust and many are specifically adapted to withstand salt spray, periodic saltwater flooding, and the islands’ well-drained sandy soil. The Outer Banks provide an important stopover for birds on the Atlantic flyway, and many species inhabit the islands year round. In addition, Outer Banks beaches provide an important nesting habitat for five endangered or threatened sea turtle species. European explorers discovered North Carolina’s barrier islands in the 16th century, although the islands were not permanently settled until the middle 17th century. By the early 19th century, shipbuilding and lumber industries were among the most successful, until forest resources were depleted. Commercial fishing eventually followed, and it expanded considerably after the Civil War. By the Great Depression, however, little industry existed on the Outer Banks. In response to the effects of a severe hurricane in 1933, the National Park Service and the Civilian Conservation Corps proposed a massive sand-fixation program to stabilize the moving sand and prevent storm waves from sweeping across the entire width of some sections of the islands. Between 1933 and 1940, this program constructed sand fencing on 185 kilometers (115 miles) of beach and planted grass seedlings, trees, and shrubs. In 1937, Congress authorized the Cape Hatteras National Seashore, which was established in 1953. The national seashore preserved one of the world’s best examples of a barrier island environment, and minimized the effect of erosion that was becoming a serious problem. In 1966, Congress authorized the Cape Lookout National Seashore to ensure that Core and Shackleford Banks would not undergo major development and could be preserved in their natural state. The rate of population growth along the Outer Banks in recent decades has been among the highest in North Carolina. More important, however, has been the growth in vacationers—in 2008, more than a quarter of a million visitors during a typical week. Municipalities now need to provide services to a transient population as much as six times as large as their permanent resident population. Although human activities have dominated the landscape changes observed on the Outer Banks for the past century or two, these changes must be understood in the context of the prevailing atmospheric, oceanic, and geologic processes that have governed the form and function of these islands for thousands of years. It is these natural processes that imbue the Outer Banks with their unique and dichotomous qualities of tranquility and tumult. In the presence of human occupation, it is these same processes that make the islands one of the highest natural-hazard risk zones along the Eastern Seaboard of the United States.

North Carolina↗

USGS2016

Influence of basin- and local-scale environmental conditions on nearshore production in the northeast Pacific Ocean

Nearshore marine habitats are productive and vulnerable owing to their connections to pelagic and terrestrial landscapes. To understand how ocean basin- and local-scale conditions may influence nearshore species, we developed an annual index of nearshore production (spanning the period 1972–2010) from growth increments recorded in otoliths of representative pelagic-feeding (Black Rockfish Sebastes melanops ) and benthic-feeding (Kelp Greenling Hexagrammos decagrammus ) nearshore-resident fishes at nine sites in the California Current and Alaska Coastal Current systems. We explored the influence of basin- and local-scale conditions across all seasons at lags of up to 2 years to represent changes in prey quantity (1- or 2-year time lags) and quality (within-year relationships). Relationships linking fish growth to basin-scale (Pacific Decadal Oscillation, North Pacific Gyre Oscillation, and multivariate El Niño–Southern Oscillation index) and local-scale (sea surface temperature, sea surface height anomalies, upwelling index, photosynthetically active radiation, and freshwater discharge) environmental conditions varied by species and current system. Growth of Black Rockfish increased with cool basin-scale conditions in the California Current and warm local-scale conditions in the Alaska Coastal Current, consistent with existing hypotheses linking climate to pelagic production on continental shelves in the respective regions. Relationships for Kelp Greenlings in the California Current were complex, with faster growth related to within-year warm conditions and lagged-year cool conditions. These opposing, lag-dependent relationships may reflect differences in conditions that promote quantity versus quality of benthic invertebrate prey in the California Current. Thus, we hypothesize that benthic production is maximized by alternating cool and warm years, as benthic invertebrate recruitment is food limited during warm years while growth is temperature limited by cool years in the California Current. On the other hand, Kelp Greenlings grew faster during and subsequent to warm conditions at basin and local scales in the Alaska Coastal Current.

Marine and Coastal Fisheries: Dynamics, Management↗

USGS1997

A new method for automated dynamic calibration of tipping-bucket rain gauges

Existing methods for dynamic calibration of tipping-bucket rain gauges (TBRs) can be time consuming and labor intensive. A new automated dynamic calibration system has been developed to calibrate TBRs with minimal effort. The system consists of a programmable pump, datalogger, digital balance, and computer. Calibration is performed in two steps: 1) pump calibration and 2) rain gauge calibration. Pump calibration ensures precise control of water flow rates delivered to the rain gauge funnel; rain gauge calibration ensures precise conversion of bucket tip times to actual rainfall rates. Calibration of the pump and one rain gauge for 10 selected pump rates typically requires about 8 h. Data files generated during rain gauge calibration are used to compute rainfall intensities and amounts from a record of bucket tip times collected in the field. The system was tested using 5 types of commercial TBRs (15.2-, 20.3-, and 30.5-cm diameters; 0.1-, 0.2-, and 1.0-mm resolutions) and using 14 TBRs of a single type (20.3-cm diameter; 0.1-mm resolution). Ten pump rates ranging from 3 to 154 mL min −1 were used to calibrate the TBRs and represented rainfall rates between 6 and 254 mm h −1 depending on the rain gauge diameter. All pump calibration results were very linear with R 2 values greater than 0.99. All rain gauges exhibited large nonlinear underestimation errors (between 5% and 29%) that decreased with increasing rain gauge resolution and increased with increasing rainfall rate, especially for rates greater than 50 mm h −1 . Calibration curves of bucket tip time against the reciprocal of the true pump rate for all rain gauges also were linear with R 2 values of 0.99. Calibration data for the 14 rain gauges of the same type were very similar, as indicated by slope values that were within 14% of each other and ranged from about 367 to 417 s mm h −1 . The developed system can calibrate TBRs efficiently, accurately, and virtually unattended and could be modified for use with other rain gauge designs. The system is now in routine use to calibrate TBRs in a large rainfall collection network at Yucca Mountain, Nevada.

Journal of Atmospheric and Oceanic Technology↗

USGS2013

Mobile Bay

Mobile Bay is the largest bay found in Alabama’s coastal area (Handley et al., 2007). It was named an Estuary of National Significance in 1995 under the U.S. Environmental Protection Agency’s (EPA) National Estuary Program (NEP), and its Comprehensive Conservation Management Plan was completed in 2002. Mobile Bay is 1,070 km 2 (413 miles 2 ) in area and 51 km (32 miles) long, making it the sixth largest estuary in the continental United States (Mobile Bay NEP, 2008). Its ecosystem provides habitat for more than 300 species of birds, 310 species of fish, 68 species of reptiles, 57 species of mammals, 40 species of amphibians, and 15 species of shrimp (Mobile Bay NEP, 1997). Mobile Bay lies between the Mississippi and Atlantic Flyways (Mobile Bay NEP, 2003). Commercial and residential development and industrial use is heavy in the Mobile Bay area. Although local growth and industrial markets support the Mobile Bay area economy, the resulting environmental damage to the very ecosystem upon which they depend remains a threat to the environment, economy, and population. The Mobile Bay ecosystem boasts high biological diversity and productivity and supports many freshwater and saltwater species of recreational and commercial importance. The great diversity of Mobile Bay reflects the diversity of Alabama, which is home to the largest number of different plant and animal species of all states east of the Mississippi River (Stein, 2002), and is bolstered by the unique climate and geographic conditions surrounding the bay. Freshwater inflow from the Mobile-Tensaw River Delta, ranging from 60,000 to 3,700,000 gallons per second (Wallace, 1996), mixes with saltwater from the Gulf of Mexico, which enters Mobile Bay via wind and tides (Burgan and Engle, 2006). Because of the unique conditions surrounding Mobile Bay, including shallow waters, a dynamic climate, and artificial hydrologic modifications—such as the construction of the Mobile Bay Causeway in the 1920s, which serves as an unintentional barrier between Delta waters north of the Causeway and saline waters south of the Causeway, the salinity of Mobile Bay is highly variable. Mobile Bay receives an average of 165 cm (65 inches) of rain per year from tropical storms, summer thunderstorms, and winter cold fronts (Stout et al., 1998). The climate and geography that have made Mobile Bay so rich in resources have also contributed to the threats surrounding its ecosystem. The extensive amount of rain in Mobile Bay creates large amounts of runoff, polluting the waters with fertilizers, chemicals, sediment, oil, trash, and sewage (Mobile Bay NEP, 1997). Tourism, ecotourism, recreational and commercial fishing, recreational boating, shipping, and chemical, pulp, and paper production are significant industries in Mobile Bay and the surrounding areas. Despite the approximate \$3 billion and 55,000 jobs these industries bring into the community (Alabama Tourism Department, 2010), the growth, development, and environmental stress they create are major threats to the Mobile Bay ecosystem. Among the nation’s states, Alabama ranks fifth in number of different species (144 endemic species), second in number of extinctions that have already occurred (90 extinct species) and fourth in number of species at risk for extinction (14.8% at risk out of 4,533 total species; Stein, 2002). Twenty-one of these threatened and endangered species are found in Mobile Bay, whose brackish waters provide a nursery area for many species of vertebrates and invertebrates. Some of these species include the Alabama sturgeon, Gulf sturgeon, heavy pigtoe mussel, inflated heel-splitter mussel, West Indian manatee, Alabama beach mouse, Perdido beach mouse, Alabama red-bellied turtle, gopher tortoise, Kemp’s ridley sea turtle, green sea turtle, loggerhead sea turtle, eastern indigo snake, flatwoods salamander, piping plover, red-cockaded woodpecker, and wood stork. Habitat loss underlies the decline of some bird species in Mobile Bay, and large mammals such as the red wolf, Florida panther, and Florida black bear are no longer found in the area. However, some rare species, such as the swallow-tailed kite, sandhill crane, and gopher tortoise can still be found (Duke and Kruczynski, 1992). The value of wetlands in Mobile Bay and the rest of the Gulf of Mexico is still being investigated. Although various monetary valuations of wetlands exist, critics remark that undervaluation of wetlands is inevitable (Mobile Bay NEP, 2008) and that estimates often do not place appropriate value on ecological services (Mitsch and Gosselink, 2000). Additionally, many estimates account only for anthropogenic values. One estimate concludes that one acre of wetlands performs \$3,000 worth of water purification each year (Mobile Bay NEP, 1997). With more than 76,890 hectares (190,000 acres) of wetlands in the Mobile Bay area, that equates to a value exceeding one-half billion dollars every year. Tourism, fishing, boating, production, and shipping are significant industries in the Mobile Bay area. More than 90% of fish landed in recreational and commercial fishing in the bay depend on bay habitat, including wetlands, for life requirements (Mobile Bay NEP, 1997). The Port of Mobile is Alabama’s only ocean-ship port (Mobile Bay NEP, 2008). Baldwin County, on the eastern side of the bay, experienced a population increase of 75% from 1990 to 2007, with an 89% increase in housing units (Mobile Bay NEP, 2008). Development and industry support the Mobile Bay economy, but they depend on the continued health, sustainability, and production of the water and living resources of the Mobile Bay ecosystem. Wetland loss, along with other forms of environmental degradation, remains a threat to the Mobile Bay ecosystem and Mobile Bay’s socioeconomic foundation.

Alabama↗

USGS2012

California State Waters Map Series — Hueneme Canyon and vicinity, California

In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California's State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 100 m) subsurface geology. The Hueneme Canyon and vicinity map area lies within the eastern Santa Barbara Channel region of the Southern California Bight. The area is part of the Western Transverse Ranges geologic province, which is north of the California Continental Borderland. Significant clockwise rotation - at least 90° - since the early Miocene has been proposed for the Western Transverse Ranges, and the region is presently undergoing north-south shortening. This geologically complex region forms a major biogeographic transition zone, separating the cold-temperate Oregonian province north of Point Conception from the warm-temperate California province to the south. The map area, which is offshore of the Oxnard plain and west of and along the trend of the south flank of the Santa Monica Mountains, lies at the east end of the Santa Barbara littoral cell, characterized by west-to-east littoral transport of sediment derived mainly from coastal watersheds. The Hueneme Canyon and vicinity map area in California's State Waters is characterized by two major physiographic features: (1) the nearshore continental shelf, and (2) the Hueneme and Mugu Submarine Canyon system, which, in the map area, includes Hueneme Canyon and parts of three smaller, unnamed headless canyons incised into the shelf southeast of Hueneme Canyon. The shelf is underlain by tens of meters of interbedded upper Quaternary shelf, estuarine, and fluvial deposits that formed as sea level fluctuated in the last several hundred thousand years. Hueneme Canyon extends about 15 km offshore from its canyon head near the dredged navigation channel of the Port of Hueneme. The canyon is relatively deep (about 150 m at the California's State Waters limit) and steep (canyon flanks as steep as 25° to 30°). Historically, Hueneme Canyon functioned as the eastern termination of the Santa Barbara littoral cell by trapping all eastward littoral drift, not only feeding the large Hueneme submarine fan but acting as the major conduit of sediment to the deep Santa Monica Basin; however, recent dredging programs needed to maintain Channel Islands Harbor and the Port of Hueneme have moved the nearshore sediment trapped by jetties and breakwaters to an area southeast of the Hueneme Canyon head. Seafloor habitats in the broad Santa Barbara Channel region consist of significant amounts of soft sediment and isolated areas of rocky habitat that support kelp-forest communities nearshore and rocky-reef communities in deep water. The potential marine benthic habitat types mapped in the Hueneme Canyon and vicinity map area are related directly to the geomorphology and sedimentary processes that are the result of its Quaternary geologic history. The two basic megahabitats in the map area are Shelf (continental shelf) and Flank (continental slope). The flat seafloor of the continental shelf in the Hueneme Canyon and vicinity map area is dynamic, as indicated by mobile sand sheets and coarser grained scour depressions. The active Hueneme Canyon provides considerable relief to the continental shelf in the map area, and its irregular morphology of eroded walls, landslide scarps, and deposits and gullies provide promising habitat for groundfish, crabs, shrimp, and other marine benthic organisms. Most invertebrates observed in the map area during camera ground-truth field operations are found on the edge of Hueneme Canyon, which may be an important area of recruitment and retention to other invertebrates and fishes. The smaller, more subtle, nonactive headless canyons located primarily on the continental slope also offer relief that provides habitat for groundfish and other organisms.

California↗

USGS2015

Categorisation of northern California rainfall for periods with and without a radar brightband using stable isotopes and a novel automated precipitation collector

During landfall of extratropical cyclones between 2005 and 2011, nearly 1400 precipitation samples were collected at intervals of 30-min time resolution with novel automated collectors at four NOAA sites in northern California [Alta (ATA), Bodega Bay (BBY), Cazadero (CZD) and Shasta Dam (STD)] during 43 events. Substantial decreases were commonly followed hours later by substantial increases in hydrogen isotopic composition ( δ 2 H VSMOW where VSMOW is Vienna Standard Mean Ocean Water) and oxygen isotopic composition ( δ 18 O VSMOW ) of precipitation. These variations likely occur as pre-cold frontal precipitation generation transitions from marine vapour masses having low rainout to cold cloud layers having much higher rainout (with concomitant brightband signatures measured by an S-band profiling radar and lower δ 2 H VSMOW values of precipitation), and finally to shallower, warmer precipitating clouds having lower rainout (with non-brightband signatures and higher δ 2 H VSMOW values of precipitation), in accord with ‘seeder–feeder’ precipitation. Of 82 intervals identified, a remarkable 100.5 &permil; decrease in δ 2 H VSMOW value was observed for a 21 January 2010 event at BBY. Of the 61 intervals identified with increases in δ 2 H VSMOW values as precipitation transitioned to shallower, warmer clouds having substantially less rainout (the feeder part of the seeder–feeder mechanism), a remarkable increase in δ 2 H VSMOW value of precipitation of 82.3 &permil; was observed for a 10 February 2007 event at CZD. All CZD and ATA events having δ 2 H VSMOW values of precipitation below −105 &permil; were atmospheric rivers (ARs), and of the 13 events having δ 2 H VSMOW values of precipitation below −80 &permil;, 77 % were ARs. Cloud echo-top heights (a proxy for atmospheric temperature) were available for 23 events. The mean echo-top height is greater for higher rainout periods than that for lower rainout periods in 22 of the 23 events. The lowest δ 2 H VSMOW of precipitation of 28 CZD events was −137.9 &permil; on 16 February 2009 during an AR with cold precipitating clouds and very high rainout with tops >6.5 km altitude. An altitude effect of −2.5 &permil; per 100 m was measured from BBY and CZD δ 2 H VSMOW data and of −1.8 &permil; per 100 m for CZD and ATA δ 2 H VSMOW data. We present a new approach to categorise rainfall intervals using δ 2 H VSMOW values of precipitation and rainfall rates. We term this approach the algorithmic-isotopic categorisation of rainfall, and we were able to identify higher rainout and/or lower rainout periods during all events in this study. We conclude that algorithmic-isotopic categorisation of rainfall can enable users to distinguish between tropospheric vapour masses having relatively high rainout (typically with brightband rain and that commonly are ARs) and vapour masses having lower rainout (commonly with non-brightband rain).

California↗

USGS2020

Spatiotemporal variability of light attenuation and net ecosystem metabolism in a back-barrier estuary

Quantifying system-wide biogeochemical dynamics and ecosystem metabolism in estuaries is often attempted using a long-term continuous record at a single site or short-term records at multiple sites due to sampling limitations that preclude long-term monitoring. However, differences in the dominant primary producer at a given location (e.g., phytoplankton versus benthic producers) control diel variations in dissolved oxygen and associated ecosystem metabolism, and they may confound metabolic estimates that do not account for this variability. We hypothesize that even in shallow, well-mixed estuaries there is strong spatiotemporal variability in ecosystem metabolism due to benthic and water-column properties, as well as ensuing feedbacks to sediment resuspension, light attenuation, and primary production. We tested this hypothesis by measuring hydrodynamic properties, biogeochemical variables (fluorescent dissolved organic matter – fDOM, turbidity, chlorophyll a fluorescence, dissolved oxygen), and photosynthetically active radiation (PAR) over 1 year at 15 min intervals at paired channel (unvegetated) and shoal (vegetated by eelgrass) sites in Chincoteague Bay, Maryland–Virginia, USA, a shallow back-barrier estuary. Light attenuation ( K dPAR ) at all sites was dominated by turbidity from suspended sediment, with lower contributions from fDOM and chlorophyll a . However, there was significant seasonal variability in the resuspension–shear stress relationship on the vegetated shoals, but not in adjacent unvegetated channels. This indicated that K dPAR on the shoals was mediated by submerged aquatic vegetation (SAV) and possibly microphytobenthos presence in the summer, which reduced resuspension and therefore K dPAR . We also found that gross primary production ( P g ) and K dPAR were significantly negatively correlated on the shoals and uncorrelated in the channels, indicating that P g over the vegetated shoals is controlled by a feedback loop between benthic stabilization by SAV and/or microphytobenthos, sediment resuspension, and light availability. Metabolic estimates indicated substantial differences in net ecosystem metabolism between vegetated and unvegetated sites, with the former tending towards net autotrophy in the summer. Ongoing trends of SAV loss in this and other back-barrier estuaries suggest that these systems may also shift towards net heterotrophy, reducing their effectiveness as long-term carbon sinks. With regards to temporal variability, we found that varying sampling frequency between 15 min and 1 d resulted in comparable mean values of biogeochemical variables, but extreme values were missed by daily sampling. In fact, daily resampling minimized the variability between sites and falsely suggested spatial homogeneity in biogeochemistry, emphasizing the need for high-frequency sampling. This study confirms that properly quantifying ecosystem metabolism and associated biogeochemical variability requires characterization of the diverse estuarine environments, even in well-mixed systems, and demonstrates the deficiencies introduced by infrequent sampling to the interpretation of spatial variability.

Maryland, Virginia↗

USGS2015

California State Waters Map Series — Offshore of Tomales Point, California

In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow (to about 200 m) subsurface geology. Tomales Bay, approximately 20-km long and 1- to 2-km wide, formed along a submerged portion of the San Andreas Fault, which forms a right-lateral transform boundary between the North American and Pacific tectonic plates. The fault juxtaposes Cretaceous granitic rock to the southwest (exposed on Tomales Point) with the Jurassic and Cretaceous Franciscan Complex to the northeast (exposed on the northeast coast of the Tomales Bay), and has an estimated slip rate of about 17 to 30 mm/yr in this area. The destructive great 1906 California earthquake (M7.8, 4/18/1906) is thought to have nucleated on the San Andreas Fault about 60 km to the south, offshore of San Francisco, with the rupture extending northward through Tomales Bay and for an additional about 230 km to the south flank of Cape Mendocino. The northwest coast of Tomales Point is characterized by steep, high (as much as 100 m), barren, granitic cliffs and a rugged shoreline with a few small pocket beaches. There has been as much as 48 m of Tomales Point cliff retreat from 1929–30 to 2002. The granite is overlain by less resistant Tertiary sandstones at Kehoe Beach, the northern end of a continuous, wide, sandy beach backed by a large coastal dune field that extends for about 20 km south to Point Reyes Head. This long beach has a mixed history of accretion and retreat since the late 1800s. Tomales Point relief is asymmetrical so that most small coastal watersheds in the map area drain eastward from Inverness Ridge into Tomales Bay. Many of these steep drainages have small sandy beaches at their mouths. The east coast of Tomales Bay is characterized by more gentle, hummocky, hilly relief underlain by the landslide-prone Franciscan Complex. Keys Creek, the most prominent small watershed entering Tomales Bay from the east, has a small subaqueous delta at its mouth. Central Tomales Bay is relatively flat and underlain by fine sand and silt. The mouth of Tomales Bay is characterized by sand waves, dunes, and flats that have formed in response to strong tidal flow. Sand Point and Dillon Beach are located at the mouth of Tomales Bay and on the southeasternmost shores of Bodega Bay, respectively. The wide beach in this area is backed by an extensive (4.8 km 2 ) sand-dune complex. The enormous volume of sand on the beach and in the dune field is derived from southward littoral drift. This sediment is trapped by Tomales Bay and Tomales Point, which function as the south end of the Bodega Bay littoral cell. The continental shelf in California’s State Waters in the Offshore of Tomales Point map area extends to water depths of about 70 m (mean slope of about 0.7°) and is characterized by extensive, rugged, rocky seafloor. Granitic seafloor has a massive and fractured texture, whereas seafloor sedimentary rock outcrops commonly form distinctive “ribs” created by differential seafloor erosion of dipping beds of variable resistance. Direct sediment supply to this shelf is minimal because littoral drift is blocked to the north by Tomales Bay and Tomales Point, and to the south by the Point Reyes headland. Circulation over the continental shelf in the map area (and in the broader northern California region) is dominated by the southward-flowing California Current, the eastern limb of the North Pacific Gyre. Associated upwelling brings cool, nutrient-rich waters to the surface, resulting in high biological productivity. The current flow generally is southeastward during the spring and summer; however, during the fall and winter, the otherwise persistent northwest winds are sometimes weak or absent, causing the California Current to move farther offshore and the Davidson Current, a weaker, northward-flowing countercurrent, to become active. As a result, net flow over the continental shelf can be more southerly during the spring and summer and more northerly during the fall and winter. Throughout the year, this part of the central California coast is exposed to four wave climate regimes—the north Pacific swell, the southern swell, northwest wind waves, and local wind waves. The north Pacific swell dominates in winter months (typically November through March), with wave heights at offshore buoys ranging from 2 to 10 m and wave periods ranging from 10 to 25 s. During summer months, the largest waves come from the southern swell, generated by storms in the south Pacific and offshore Central America. Characteristically, these swells have smaller wave heights (0.3 to 3 m) and similarly long periods (range 10 to 25 s). Northwest wind waves affect the coast throughout the year, while local wind waves are most common from October to April. These two wind-wave regimes typically have wave heights of 1 to 4 m and short periods (3 to 10 s). Potential marine benthic habitats in the Offshore of Tomales Point map area range from unconsolidated continental-shelf sediment, to rocky continental-shelf substrate, to unconsolidated estuary sediments. Rocky-shelf outcrops and rubble are considered to be promising potential habitats for rockfish and lingcod, both of which are recreationally and commercially important species. Dynamic bedforms, such as the sand waves at the mouth of Tomales Bay, are considered potential foraging habitat for juvenile lingcod and possibly migratory fishes, as well as for forage fish such as Pacific sand lance.

California↗

USGS2022

Evaluation of the Bushy Park Reservoir three-dimensional hydrodynamic and water-quality model, South Carolina, 2012–15

The Bushy Park Reservoir is a relatively shallow impoundment in southeastern South Carolina. The reservoir, located under a semi-tropical climate, is the principal water supply for the city of Charleston, South Carolina, and the surrounding areas including the Bushy Park Industrial Complex. Although there was an adequate supply of freshwater in the reservoir in 2022, water-quality concerns are present over taste-and-odor and saltwater-intrusion issues. From 2013 to 2015, the U.S. Geological Survey (USGS), in cooperation with the Charleston Water System, engaged in a multi-year study of the hydrology and hydrodynamics of Bushy Park Reservoir to better understand factors affecting water-quality conditions in the reservoir. As part of this study, Charleston Water System worked with Tetra Tech, Inc., a consulting and engineering firm, to develop a Bushy Park Reservoir hydrodynamic and water-quality modeling framework, built upon earlier efforts by both Tetra Tech and the U.S. Army Corps of Engineers. At the completion of the new modeling framework, the USGS was requested to evaluate the calibrated hydrodynamic and water-quality model. The Bushy Park Reservoir Environmental Fluid Dynamics Code (EFDC) model was calibrated for the time period from January 1, 2012, to December 31, 2015. The general modeling approach for the newly revised modeling framework, as briefly detailed in this report, was developed with EFDC. The EFDC is a grid-based modeling package that can simulate three-dimensional flow, transport, and water quality in surface-water systems. This report evaluated the capacity of Tetra Tech’s Bushy Park EFDC model to simulate water discharge, water circulation, surface elevations, temperature, salinity, and other water-quality parameters. The USGS model review focused specifically on the following criteria: (1) determine if the model, with additional effort, could be developed into an adequate planning tool for Bushy Park Reservoir; (2) assess the capacity of the model to specifically address water-quality issues in the reservoir related to taste-and-odor and saltwater intrusions; and, (3) evaluate three preliminary water-management scenarios related to reduced water withdrawals in the reservoir and the effect on saltwater intrusion. Overall, the model was able to simulate discharge, flow velocity, and water-surface elevations with generally good agreement between the simulated and measured values. Specifically, the model was able to demonstrate good agreement for discharge at two USGS continuous discharge locations (USGS station 02172002; USGS station 02172040), with Wilmott index of agreements of 0.86 and 0.75, respectively. A total of seven USGS streamgages, located on the West Branch of the Cooper River, Durham Canal, and the Cooper River, were available for water-surface elevations, with index of agreements ranging from 0.74 to 0.99. However, model-simulated water-surface elevation ranges were appreciably high (compared to measured ranges) for two locations near Pinopolis Dam, farthest upstream on the West Branch of the Cooper River. This result may indicate that too much simulated tidal energy propagated through the model domain. For water temperature, 16 calibration stations were available for at least part of the 4-year simulation. The index of agreement range for temperature comparisons was from 0.95 to 1.00, indicating excellent agreement between the measured and simulated results. One of the primary future applications for the Bushy Park Reservoir EFDC model is to determine the extent of saltwater intrusions. A wide range in the salinity prediction quality was simulated with the model. The prediction quality ranged from an index of agreement of 0.15 at Cooper River approximately 2.75 miles southeast of the Tee, South Carolina, to 0.92 at West Branch Cooper River near Moncks Corner, South Carolina. Although the model did not accurately simulate some of the larger salinity deviations resulting during individual hydrologic events, the seasonal salinity trends were adequately simulated with the model during the study period (2012–15). Therefore, it may be difficult to simulate extreme hydrologic events, such as during large storms, where high salinity water is exchanged with Bushy Park Reservoir. There was agreement in model simulation with the measured data either on the quantitative index of agreement values or qualitative agreement in the seasonal salinity data trends. For water quality, the index of agreement values were generally low for total nitrogen, ammonia, nitrate, total Kjeldahl nitrogen, total phosphorus, and orthophosphate. Although general trends were adequately simulated at specific stations, particularly for Bushy Park Reservoir, the model-simulated fit was low across all the constituents described above with index of agreements usually below 0.50. A limitation for simulating nutrient concentrations across the model domain was the lack of characterization for the constituents directly entering Bushy Park Reservoir, or the lack of data directly attributed to the boundary condition (for example, the Cooper River). The other two calibrated water-quality constituents (besides the nutrients mentioned above) were dissolved oxygen and chlorophyll a . Dissolved oxygen varied from index of agreement values from 0.58 to 0.94 for 11 stations, generally indicating agreement with the available measured data. Chlorophyll a , calibrated for seven stations, had a wider range from 0.11 to 0.74 for the index of agreement. With the current modeling framework, taste-and-odor events, related to cyanobacterial blooms, cannot be directly simulated. However, indirect estimates of cyanobacteria concentrations may be obtained by using the chlorophyll a model outputs, which represent total phytoplankton biomass, and the phytoplankton biovolume data by group (diatoms, green algae, cyanobacteria and others) collected from 2012 to 2015. For the Bushy Park Reservoir modeling framework to be used directly for taste-and-odor issues, cyanobacteria must be simulated and calibrated based on observations of cyanobacteria biomass concentrations. In addition to the cyanobacteria sampling conducted within the reservoir between 2012 and 2015, the new model calibration would also require new algae biomass data-collection efforts to characterize the external sources of cyanobacteria entering the Bushy Park Reservoir from tributaries, as well as the internal cycling, production, and decay of cyanobacteria in the hydrologic system. Further improvements to the EFDC model would include expanding the collection of boundary condition datasets, such as water-quality monitoring to determine improved nutrient loads into the model domain. Along with improved water-quality monitoring for the major boundary conditions, continuous discharge, for both Foster Creek and the Back River, would further constrain the flow balance and the loads into Bushy Park Reservoir. In addition to better boundary-condition characterization, it is important to better characterize possible shortcomings specifically to the model domain, such as the grid resolution, bathymetry, and numerical hydrodynamic errors. Further consideration of the model may involve a sensitivity analysis to determine if errors in the simulation outputs, such as discharge, water-surface elevations, and salinity, were more likely caused by poor boundary condition characterization or, specifically, the model setup. Three model scenarios were run with the revised Bushy Park Reservoir model: (1) reduced withdrawals from one of the large intake-discharge locations for Bushy Park Reservoir, the Williams Station; (2) elevated (above background levels) ocean water level causing saltwater intrusion from the ocean through Durham Canal into Bushy Park Reservoir; and (3) overtopping of the Back River Dam at the southernmost end of Bushy Park Reservoir. For the reduced withdrawals scenarios, the largest shift in flow resulted near the Williams Station intake, with the next largest flow change at the southern end of Bushy Park Reservoir, and a net increase in flow out of the Bushy Park Reservoir to the Cooper River by way of the Durham Canal. The effect resulting from scenario 3 on water quality and salinity was small, with larger increases for dissolved oxygen than other constituents at several monitoring stations. For the two scenarios related to saltwater intrusion (including dam overtopping), the changes in salinity generally were found to dissipate in the following 2 weeks and generally back to baseline salinity conditions within 3 months. This result did vary depending on the severity of the storm or length of the dam overtopping event.

South Carolina↗

USGS1993

1993 Annual Report: San Francisco estuary regional monitoring program for trace substances

This first annual report of the San Francisco Estuary Regional Monitoring Program contains the results of monitoring measurements made in 1993. Measurements of conventional water quality parameters and trace contaminant concentrations were made at 16 stations throughout the Estuary three times during the year: the wet period (March), during declining Delta outflow (May), and during the dry period (September). Water toxicity tests were conducted at 8 of those stations. Measurements of sediment quality and contaminant concentrations were made at the same 16 stations during the wet and dry sampling periods. Sediment toxicity was measured at 8 of those stations. Transplanted, bagged bivalve bioaccumulation and condition was measured at 11 stations during the wet and dry sampling periods. Water Monitoring. Total or near-total (dissolved + particulate, see text) arsenic, cadmium, selenium, and dissolved (0.45 µm filtered) arsenic, cadmium, copper, nickel, silver, and zinc in water were highest in the South Bay. In general, dissolved metals in water were usually lowest in the Central Bay due to ocean influences. Near-total nickel and total mercury in water were highest in the northern estuary (San Pablo and Suisun Bays). Dissolved chromium and lead were highest at the Sacramento and San Joaquin River confluence stations. Six of the ten dissolved trace metals were highest in March during high runoff. Dissolved and total arsenic, selenium, and near-total cadmium were highest in September. Concentrations of trace organic contaminants are reported for the March sampling period. Total PAHs and PCBs were highest in the South Bay, but PCBs were also high in the Napa River. Dissolved PAHs were highest in the Central Bay, and dissolved PCBs were highest in the Napa River. Total and dissolved pesticides were highest in the Sacramento River and in the Extreme South Bay. Concentrations of trace elements in water (except selenium) were usually closely related with other environmental parameters. Total or near-total metals concentrations in water were most often associated with the amount of particulate material (TSS) in the water. Dissolved concentrations were usually associated with salinity or dissolved organic carbon (DOC) content. Dissolved PAHs were well correlated with TSS, but dissolved and total trace organic contaminants were poorly correlated with other water parameters. Based on deviations from conservative mixing of fresh and salt water, three different patterns of possible sources of metals were identified in 1993. For dissolved chromium and lead, rivers and local runoff appeared to be important sources. For dissolved arsenic, cadmium, copper, and nickel year-round inputs from the South Bay appeared to be important sources. Dissolved mercury, selenium, and zinc were associated with local runoff in the South Bay during the wet period. Dissolved silver did not fit any of these patterns. Although most contaminant concentrations were below water quality objectives, several trace contaminants were above the objectives at some stations. Comparisons to water quality objectives are used as a guide for evaluation of contaminant concentrations, but there are some differences in the way the RMP data are measured and that prescribed for regulatory purposes (see text). Concentrations of 5 metals in water were above EPA or Regional Basin Plan water quality objectives at six stations (see Table 30). Most of these elevated levels occurred at the northern estuary stations. Total PCB concentrations were above EPA human health objectives at all RMP stations. The pesticides chlordane, dieldrin, and DDTs were above the EPA objectives at several RMP stations, particularly at the northern-most, and river confluence stations. Although some of the contaminant concentrations were above water quality objectives, water toxicity tests (96 hour algal growth and 48 hour bivalve larval development tests) did not indicate toxicity (sometimes inconclusive) associated with the water samples collected at any of the RMP stations in 1993. Exposure to Bay San Francisco Estuary Regional Monitoring Program Regional Monitoring Program 1993 Report ii water actually enhanced algal growth at most stations. In addition to the Estuary-wide sampling, the Sacramento and San Joaquin Rivers were sampled upstream from their confluence. Stations in each river were sampled six times over a 6 week period of high flows. In the Sacramento River, seven of the ten dissolved metals measured had concentrations lower than those measured at the river confluence stations. Some metals concentrations in the San Joaquin River were higher, and some were lower than concentrations from the river confluence station. Metals concentrations in the Sacramento River were poorly related to river flow because the station at Rio Vista is under considerable tidal influence. In the San Joaquin River, flows were inversely related to 7 of 10 total metals concentrations. Sediment Monitoring. Concentrations of silver, mercury, and lead in sediment were highest in the South Bay. However, concentrations of most trace metals in sediments were highest in the northern estuary at stations with the finest (silt, clay) sediments. The northern estuary stations with the coarsest (sand, shell) sediments generally had the lowest metals concentrations. There were differences in concentrations of cadmium, lead, and selenium in sediments between the sampling periods, but no consistent trend as to which sampling period had higher values. In September, PAHs and PCBs in sediments were highest in the Central Bay, but pesticides in sediments were highest in the northern estuary and Extreme South Bay. NOAA’s Median Effects Ranges (ERM) for sediments were used as a guide for evaluation of sediment contaminant concentrations. Nickel was the only trace contaminant in sediment above the ERM guidelines, and it was high at all RMP stations. These high levels are probably due to natural, geologic sources. Although sediment contaminant concentrations were below ERMs, sediment toxicity tests (10 day amphipod mortality, and 48 hour bivalve larval development in elutriates) indicated toxicity at all stations tested. Sediment factors that could have caused the toxicity were not investigated. Bivalve Bioaccumulation. Mussels, oysters, and freshwater clams were transplanted to the RMP stations to evaluate bioaccumulation of trace substances. Trace metals were bioaccumulated at nearly all RMP stations. However, arsenic, lead, and mercury did not appear to bioaccumulate. There was generally more bioaccumulation during the dry season than during the wet season. In September, PAHs, PCBs, and pesticides accumulated in all samples. Bioaccumulation of PAHs and pesticides was generally highest at the river confluence stations, and the Napa River. PCBs accumulated most at Redwood Creek. There were substantial differences in the degree of bioaccumulation among the species. Oysters appeared to accumulate higher concentrations of trace metals than the other species, especially copper, which may be a natural phenomenon. There are no established tissue contaminant standards for trace metal and organic contaminants. Therefore, comparisons to Median International Standards (MIS) for human consumption, or U.S. Food and Drug Administration (USFDA) action levels for trace organics are used to evaluate the bioaccumulation results. Concentrations of selenium were higher than MIS guidelines at all stations during the wet season. Other trace metal concentrations were higher than MIS guidelines at various stations during one or the other sampling period. However, none of the bivalves contained concentrations above the USFDA or National Academy of Sciences (NAS) guidelines for trace organic contaminants. The transplanted bivalves survived well at all stations except in the Napa River where less than 35% survived during both sampling seasons. Measures of bivalve condition (dry weight, shell volume) indicated that bivalves deployed in the Central Bay grew significantly, but those at most other stations actually lost weight. Whether these differences were due to natural causes such as salinity or food supply, or to contamination, was not determined. Pilot Studies. Two pilot monitoring studies were conducted in 1993. A pilot study of Estuary hydrography and phytoplankton was conducted by scientists from the U.S. Summary Geological Survey in Menlo Park and U.C. Davis. Water column profiles at up to 37 stations were monitored along a transect of the Estuary run monthly between the South Bay and the Delta. The primary objective of this study was to define physical (salinity, temperature, suspended particulate matter, and light penetration), chemical (dissolved oxygen) and biological (chlorophyll a) characteristics of Estuary water that may influence other chemical and biological reactions. A second objective was to investigate planktonic indicators of ecosystem structure and function. The data collected in 1993 showed the extent and duration of the spring phytoplankton bloom in the South Bay, other localized blooms in the northern estuary, the stratification and mixing associated with the entrapment zone in the northern estuary, and mixing in the Estuary resulting from the high rainfall in 1993. Knowledge of the duration and extent of these natural features of the Estuary provide context for interpretation of the RMP contaminant data collected only 3 times per year. Another pilot study of suspended sediment transport processes was conducted by the USGS in Sacramento. This study used continuous recording sensors at Point San Pablo and the Bay Bridge to measure the amount of suspended sediment in the water at mid-depth and near the bottom, as well as tide height. The objectives of this study were to estimate which factors determine suspended solids concentrations in the Central Bay and to collect time series of suspended solids that are appropriate for continuous monitoring of suspended solids and for calibration and validation of numerical models. The investigators determined that spring tides accounted for most of the variation in suspended solids concentrations at the stations monitored, not runoff from the Sacramento or San Joaquin Rivers, or semidiurnal and diurnal tides. Comparisons were also made between measurements made by the continuous recordings and the RMP samples collected during the regular monitoring cruises. The different ways of measuring TSS were generally comparable, however only 3 measurements per year as made by the RMP could not provide the information of TSS variation actually occurring in the Estuary. This information is important because as shown by the RMP data, total contaminant concentrations in Estuary water is largely dependent on the TSS in the water. This implies that the RMP measurements alone cannot determine accurately the range of contaminant concentrations without better characterizing the dynamics of TSS. The RMP Pilot Studies are important to the developing RMP because they will help put RMP measurements into the perspective of Estuary processes and mechanisms at other time scales. The studies can relate those processes to the RMP measurements and will facilitate revision of sampling design and interpretation. Summaries of other monitoring activities pertinent to regional monitoring are also included in the Report: a description of the Regional Board’s Bay Protection Studies, the Sacramento Coordinated Monitoring Program, and a wetlands monitoring plan are included.

California↗