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USGS2019

Tampa Bay Ocean and Coastal Acidification Monitoring Quality Assurance Project Plan

Coastal acidification caused by eutrophication, freshwater inflow, and upwelling is already affecting many estuaries worldwide and can be exacerbated by ocean acidification that is caused by increasing carbon dioxide in the atmosphere. Effective management, mitigation, and (or) adaptation to the effects of coastal and ocean acidification require careful monitoring of the resulting changes in seawater chemistry. Local, regional, and national agencies and institutions organizing acidification-monitoring and research efforts work toward standardizing data collection and reporting protocols so that data can be shared and compared across regions and synthesized into national assessments. This document describes a Quality Assurance Project Plan for the collection and reporting of seawater chemical and physical data using standardized methods and published best practices relevant for monitoring coastal and ocean acidification. The plan specifically addresses procedures for a joint partnership, the Tampa Bay Ocean and Coastal Acidification Monitoring project, conducted by the U.S. Geological Survey, the U.S. Environmental Protection Agency, and the Tampa Bay Estuary Program in the Tampa Bay estuary, Florida. The plan describes recommended procedures for project organization, sampling process design and methods, data-quality objectives and criteria, data validation and management procedures, and project deliverables.

Florida↗
USGS2020

Impacts of periodic dredging on macroinvertebrate prey availability for benthic foraging fishes in central San Francisco Bay, California

Background Because of its importance for species covered under Federal Fishery Management Plans (FMPs), the San Francisco Bay (SFB) estuary has been designated as Essential Fish Habitat (EFH) under the Magnuson-Stevens Fishery Conservation and Management Act (MSA; 16 United States Code §18559b). Within this estuary, benthic macroinvertebrate communities provide important prey resources for many economically significant fish species that rely on EFH. Periodic maintenance dredging can impact benthic communities; however, there is a lack of scientific information specific to SFB regarding dredging effects on macroinvertebrates in fish foraging areas. In addition, rates of benthic community recolonization and recovery following dredging and subsequent effects on foraging fish are unknown. For this reason, it is difficult for regulatory and resource agencies to determine the impacts of maintenance dredging. Thus, the National Marine Fisheries Service (NMFS) and the consortium of agencies (U.S. Environmental Protection Agency [EPA], U.S. Army Corp of Engineers [USACE], San Francisco Regional Water Quality Control Board [SFRWQCB], and San Francisco Bay Conservation and Development Commission [BCDC]) that make up the San Francisco Bay Long Term Management Strategy for Dredging (LTMS) identified a study of dredging impacts on SFB fish foraging habitat as one of their highest priorities in their 2011 Programmatic EFH Agreement (U.S. Army Corp of Engineers and U.S. Environmental Protection Agency, 2011). The LTMS agencies identified the region of interest as shallow (<13 feet [<4 meters (m)] mean lower low water [MLLW]), soft-bottom (silt/clay soil texture) areas in the Central Bay of SFB that were periodically dredged (every 1–3 years). Fish species of interest were compiled by NMFS and included those managed by the Pacific Groundfish, Pacific Salmon, and Coastal Pelagic FMPs (pursuant to the MSA) as well as those listed under the California State or Federal Endangered Species Act (ESA; 16 U.S.C. §1531–1544) as threatened or endangered. Target species included leopard shark ( Triakis semifasciata ), big skate ( Raja binoculata ), English sole ( Parophrys vetulus ), starry flounder ( Platichthys stellatus) , brown rockfish ( Sebastes auriculatus ), green sturgeon ( Acipenser medirostris ; threatened species under Federal ESA), northern anchovy ( Engraulis mordax ), longfin smelt ( Spirinchus thaleichthys, threatened under California ESA), and Pacific sardine ( Sardinops sagax ). In addition, Dungeness crab ( Cancer magister ), California halibut ( Paralichthys californicus ), and white sturgeon ( Acipenser transmontanus ) also were included because they are substantial contributors to the California State fishery. To address LTMS priorities, U.S. Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station (hereafter USGS) conducted a multi-phased project including an initial literature review, study design, pilot study, and implementation of a full study. The overarching goal was to assess the effects of periodic dredge operations (every 1–3 years) on benthic habitat for foraging fish in the Central Bay, with emphasis on the foraging requirements of target fish species and analyses of benthic macroinvertebrates in dredged areas compared to adjacent undredged reference areas. The USGS partnered with University of California, Davis, fisheries expert James Hobbs to synthesize existing knowledge of fish foraging ecology and review benthic infauna community composition in SFB with a focus on the Central Bay. The literature review (Phase I; De La Cruz and others, 2016) addressed key questions identified by the LTMS on benthic foraging fish in the study area, including the following: (1) What are target fish eating? (2) What are the seasonal differences in prey items and macroinvertebrate assemblages? (3) What are the annual differences in prey items and macroinvertebrate assemblages? (4) What are the predominant macroinvertebrate functional groups from the perspective of fish foraging? Phase II consisted of creating a framework for a functional assessment of maintenance dredging effects on foraging fish and drafting a full study design (De La Cruz and others, 2017), which was then tested in the Phase III pilot study. The Phase IV full study incorporated lessons learned from the pilot study. Here we focus on the results of the full study and implications for benthic foraging fishes.

California↗
USGS1979

Particulate organic carbon in San Francisco Bay, California, 1971-1977

The organic-carbon content of suspended particulate matter is determined by wet oxidation and analysis of the resulting CO 2 with an infrared analyzer. Modifications of methods and improved designs of apparatus are presented. Results of particulate organic carbon (POC) analyses from 1971 through 1977 show that concentrations in North San Francisco Bay (estuary) typically decrease from the delta of the Sacramento and San Joaquin rivers to Golden Gate (seaward). Median winter (November through February) concentrations decrease from 85 to 30 µ g-at./L seaward. During March through October, median concentrations are higher and ranges are wider. Concentrations frequently exceed 250 µ g-at./L in the upper estuary. POC concentrations in South San Francisco Bay are highest at the southern reach. POC is more abundant during March through October than during winter, but POC is not as abundant in South San Francisco Bay as it is in the estuary.

California↗
USGS1981

Composition of tidal flat sediments, Willapa Bay, Washington

The purpose of this study was to characterize the modern sediments of sandy tidal flats in Willapa Bay, Washington based on their composition. Generally, clay comprises less than five percent of the sediment. Clay content increases upslope and up-estuary. Principal clay minerals are montmorillanite, illite, and chlorite; two clay mineral suites are present: (1) muddy flat suite with clay containing 44% montmorillonite, and (2) sandy flat suite with clay composition of 88% montmorillonite. Heavy minerals make up approximately four percent of the tidal flat sediment. Distribution of heavy minerals reflect their source with (1) heavy minerals most abundant near the beach on flats to the north where they were eroded out of terrace deposits, and (2) relatively greater heavy mineral concentrations (supplied by the Naselle River) across the entire flat to the south. The composition of the heavy mineral suite is mainly clinopyroxene, orthopyroxene, hornblende, epidote, and opaque minerals. This mineral suite represents several sources including rivers, ocean and ocean beaches, and reworked local Tertiary and Quaternary deposits. Tidal flat sediments are approximately 90% light minerals, mostly quartz. The light fraction also contains small quantities of lithic fragments, pumice, vegetation, and biogenic shell fragments. Tertiary and Quaternary terrace deposits are the major source of most of the light material. Fossils make up less than one percent of the bottom sediment. Two foram assemblages are present: (1) a modern shallow-water assemblage characterized by Trochammina inflata, found mainly in muddy flats near rivers, and (2) a relic deep-water assemblage (Eocene to Cretaceous) characterized by such species as Bathysiphon and Cyclammina found predominantly on the sandy flats. Macrofossils consists of shells of the modern tidal flat mollusc assemblage. Organic sediments were mostly carbon (1%). The highest concentrations of organic carbon are associated with muddy sediments near the Palix River and Pickernell Creek; overall, organic carbon concentration increased up-estuary. C/N ratios are transitional between open marine environments and marsh deposits of estuaries.

Washington↗
USGS1982

Aliphatic Hydrocarbons in Surface Sediments of Willapa Bay and Grays Harbor, Washington

Willapa Bay and Grays Harbor are two adjacent estuaries along the coast of Washington state. Willapa Bay is a recreational area minimally affected by industry; Grays Harbor, on the other hand, is moderately industrialized. Aliphatic hydrocarbons in surface sediments from these two estuaries reflect the differences in human activities. For example, the mean concentration of aliphatic hydrocarbons for seven stations in Willapa Bay is 1,000 ?g/g (relative to organic carbon) while in Grays Harbor this mean concentration for six stations is 1,900 ?g/g. The difference is attributed mainly to the greater urban and industrial pollution in Grays Harbor. The gas chromatographic records of aliphatic hydrocarbons also reflect the extent of hydrocarbon pollution by the presence of a chromatographically unresolved mixture of hydrocarbons. This kind of mixture is more evident in sediments from Grays Harbor, and in both estuaries it is more concentrated in sediments collected nearest to urban centers.

Open-File Report↗
USGS1989

U.S. Geological Survey second national symposium on Water quality; abstracts of the technical sessions, Orlando, Florida, November 12-17, 1989

The U.S Geological Survey (USGS) compiled and analyzed existing hydrologic and water-quality data from over 200 stream and estuary stations of the Abemarle-Pamlico estuarine system (A/P) to identify long-term temporal and spatial trends. The dataset included seven stations of the USGS National Stream Quality Accounting Network, two stations of the National Atmospheric Precipitation Deposition monitoring network, stations of the N.C. Department of Natural Resources and Community Development, and stations from 25 reports by individual investigators. Regression-residuals analysis, the seasonal Kendall's Tau test for trends, and graphical analysis using annual box plots were employed to determine trends. Profound change has occurred in the water quality of the A/P area over the last 30 years. Analysis of water-quality data upstream from the estuaries indicates increases of discharge-adjusted values of specific conductance, alkalinity, phosphorous, hardness, chloride, and dissolved solids. In the estuaries, pH is increasing except in the Pamlico River, where it is decreasing. There is a generalized decrease in suspended inorganic material in the system. Salinities are decreasing for sections of the Pamlico River, and increasing for parts of Albemarle Sound. Nitrogen concentrations are decreasing except in the Pamlico River, where they are increasing. Phosphorus concentrations are increasing in the Pamlico River and decreasing elsewhere. Annual average data show that nitrogen is the limiting nutrient in the Neuse and Pamlico Rivers. Phosphorus is limiting in the rest of the area. Chlorophyll-a levels are increasing in parts of the Neuse and Pamlico Rivers and decreasing in parts of the Chowan River. To evaluate the effect of basin characteristics on water quality, linear correlation was used. Agricultural crop variables produced the most correlations with water-quality data. Fertilizer usage had little detectable relation to water quality in the study area. In the section of the Pamlico River near Aurora, relations between employment, road mileages, and water quality indicated effects of development in the area.

Open-File Report↗
USGS2007

Concentrations and Loads of Organic Compounds and Trace Elements in Tributaries to Newark and Raritan Bays, New Jersey

A study was undertaken to determine the concentrations and loads of sediment and chemicals delivered to Newark and Raritan Bays by five major tributaries: the Raritan, Passaic, Rahway, Elizabeth, and Hackensack Rivers. This study was initiated by the State of New Jersey as Study I-C of the New Jersey Toxics Reduction Workplan for the New York-New Jersey Harbor, working under the NY-NJ Harbor Estuary Program (HEP) Contaminant Assessment and Reduction Program (CARP). The CARP is a comprehensive effort to evaluate the levels and sources of toxic contaminants to the tributaries and estuarine areas of the NY-NJ Harbor, including Newark and Raritan Bays. The Raritan and Passaic Rivers are large rivers (mean daily discharges of 1,189 and 1,132 cubic feet per second (ft3/s), respectively), that drain large, mixed rural/urban basins. The Elizabeth and Rahway Rivers are small rivers (mean daily discharges of 25.9 and 49.1 ft3/s, respectively) that drain small, highly urbanized and industrialized basins. The Hackensack River drains a small, mixed rural/urban basin, and its flow is highly controlled by an upstream reservoir (mean daily discharge of 90.4 ft3/s). These rivers flow into urbanized estuaries and ultimately, to the Atlantic Ocean. Each of these tributaries were sampled during two to four storm events, and twice each during low-flow discharge conditions. Samples were collected using automated equipment installed at stations adjacent to U.S. Geological Survey streamflow-gaging stations near the heads-of-tide of these rivers. Large-volume (greater than 50 liters of water and a target of 1 gram of sediment), flow-weighted composite samples were collected for chemical analysis using filtration to collect suspended particulates and exchange resin (XAD-2) to sequester dissolved contaminants. Composite whole-water samples were collected for dissolved polycyclic aromatic hydrocarbons (PAH) and for trace element analysis. Additional discrete grab samples were collected throughout each event for trace-element analysis, and multiple samples were collected for suspended sediment (SS), particulate carbon (POC), and dissolved organic carbon (DOC) analysis. The suspended sediment and exchange resin were analyzed for 114 polychlorinated biphenyls (PCBs, by US EPA method 1668A, modified), seven 2,3,7,8-substituted chlorinated dibenzo-p-dioxins (CDD) and 10 dibenzo-p-difurans (CDF) (by US EPA method 1613), 24 PAHs (by low-resolution isotope dilution/mass-spectral methods), 27 organo-chlorine pesticides (OCPs) (by high resolution isotope dilution/mass-spectral methods), and the trace elements mercury (Hg), methyl-mercury (MeHg), lead (Pb), and cadmium (Cd). Isotope dilution methods using gas chromatography and high-and low-resolution mass spectral (GC/MS) detection were used to accurately identify and quantify organic compounds in the sediment and water phases. Trace elements were measured using inductively coupled plasma-mass spectrometry and cold-vapor atomic fluorescence spectrometry methods. The loads of sediment, carbon, and chemicals were calculated for each storm and low-flow event sampled. Because only a few storm events were sampled, yearly loads of sediment were calculated from rating curves developed using historical SS and POC data. The average annual loads of sediment and carbon were calculated for the period 1975-2000, along with the loads for the selected water years being modeled as part of the New York New Jersey Harbor Estuary Program CARP. Comparison of loads calculated using the rating curve method to loads measured during the sampled storm events indicated that the rating curve method likely underpredicts annual loads. Average annual loads of suspended sediment in the tributaries were estimated to be 395,000 kilograms per year (kg/yr) in the Hackensack River, 417,000 kg/yr in the Elizabeth River, 882,000 kg/yr in the Rahway River, 22,700,000 kg/yr in the Passaic River, and 93,100,000 kg/yr in the Raritan River. Averag

Scientific Investigations Report↗
USGS2014

Integrated synoptic surveys of the hydrodynamics and water-quality distributions in two Lake Michigan rivermouth mixing zones using an autonomous underwater vehicle and a manned boat

The U.S. Geological Survey (USGS), in cooperation with the National Monitoring Network for U.S. Coastal Waters and Tributaries, launched a pilot project in 2010 to determine the value of integrated synoptic surveys of rivermouths using autonomous underwater vehicle technology in response to a call for rivermouth research, which includes study domains that envelop both the fluvial and lacustrine boundaries of the rivermouth mixing zone. The pilot project was implemented at two Lake Michigan rivermouths with largely different scales, hydrodynamics, and settings, but employing primarily the same survey techniques and methods. The Milwaukee River Estuary Area of Concern (AOC) survey included measurements in the lower 2 to 3 miles of the Milwaukee, Menomonee, and Kinnickinnic Rivers and inner and outer Milwaukee Harbor. This estuary is situated in downtown Milwaukee, Wisconsin, and is the most populated basin that flows directly into Lake Michigan. In contrast, the Manitowoc rivermouth has a relatively small harbor separating the rivermouth from Lake Michigan, and the Manitowoc River Watershed is primarily agricultural. Both the Milwaukee and Manitowoc rivermouths are unregulated and allow free exchange of water with Lake Michigan. This pilot study of the Milwaukee River Estuary and Manitowoc rivermouth using an autonomous underwater vehicle (AUV) paired with a manned survey boat resulted in high spatial and temporal resolution datasets of basic water-quality parameter distributions and hydrodynamics. The AUV performed well in these environments and was found primarily well-suited for harbor and nearshore surveys of three-dimensional water-quality distributions. Both case studies revealed that the use of a manned boat equipped with an acoustic Doppler current profiler (ADCP) and multiparameter sonde (and an optional flow-through water-quality sampling system) was the best option for riverine surveys. To ensure that the most accurate and highest resolution velocity data were collected concurrently with the AUV surveys, the pilot study used a manned boat equipped with an ADCP. Combining the AUV and manned boat datasets resulted in datasets that are essentially continuous from the fluvial through the lacustrine zones of a rivermouth. Whereas the pilot studies were completed during low flows on the tributaries, completion of surveys at higher flows using the same techniques is possible, but the use of the AUV would be limited to areas with relatively low velocities (less than 2 feet per second) such as the harbors and nearshore zones of Lake Michigan. Overall, this pilot study aimed at evaluation of AUV technology for integrated synoptic surveys of rivermouth mixing zones was successful, and the techniques and methods employed in this pilot study should be transferrable to other sites with similar success. The use of the AUV provided significant time savings compared to traditional sampling techniques. For example, the survey of outer Milwaukee Harbor using the AUV required less than 7 hours for approximately 600 profiles compared to the 150 hours it would have taken using traditional methods in a manned boat (a 95 percent reduction in man-hours). The integrated datasets resulting from the AUV and manned survey boat are of high value and present a picture of the mixing and hydrodynamics of these highly dynamic, highly variable rivermouth mixing zones from the relatively well-mixed fluvial environment through the rivermouth to the stratified lacustrine receiving body of Lake Michigan. Such datasets not only allow researchers to understand more about the physical processes occurring in these rivermouths, but they provide high spatial resolution data required for interpretation of relations between disparate point samples and calibration and validation of numerical models.

Wisconsin↗
USGS2015

Evaluation of the effects of sewering on nitrogen loads to the Niantic River, southeastern Connecticut, 2005-2011

Nitrogen concentration data were collected from 20 wells near the Niantic River Estuary, during 18 sampling periods from 2005 through 2011, as part of a study to determine changes in nitrogen concentrations and loads as a result of sewering on the Pine Grove peninsula in Niantic, Connecticut. The Pine Grove peninsula area is a neighborhood of 35 acres containing 172 residences with onsite wastewater treatment systems at the beginning of the study in 2005. From 2008 through 2009, the residences were connected to a newly installed sewer system. Water-quality data collection continued from 2010 through 2011, after the sewers were installed. The peninsula is underlain by glacial stratified deposits. The freshwater in this aquifer ranges from 10 to 45 feet (ft) in thickness and overlies saline groundwater. The mean water-table altitude was from 0.09 to 0.97 ft above the North American Vertical Datum of 1988, with a horizontal hydraulic gradient of 0.0004 to 0.0005. Initial sampling of the wells included analysis for nutrients, major ions, boron, bromide, and dissolved gases. Concentrations of nitrate plus nitrite nitrogen from the initial sampling ranged from 0.94 to 20 milligrams per liter (mg/L) in samples collected spatially and with depth in the aquifer. The mean concentration of total dissolved nitrogen before the sewers were installed was 7.5 mg/L, and dissolved gas analyses indicated little or no denitrification in the aquifer. Chloride to bromide ratios and boron analysis of the initial water samples confirmed that wastewater was a source of groundwater recharge to most of the wells. Annual recharge from onsite wastewater-disposal systems in 2006 was 4.98 inches, based on analysis of water-use data. Concentrations of total dissolved nitrogen decreased following sewering in samples from most of the wells that were identified as having nitrogen related to wastewater discharge. Concentrations of total dissolved nitrogen in individual wells decreased by as much as 11.7 mg/L between the periods before and after the sewers were installed, and the mean concentration of total dissolved nitrogen in all wells decreased by 2.3 mg/L to a mean concentration of 5.2 mg/L. Nitrogen loads from groundwater in the Pine Grove peninsula area were estimated for three time periods by using the measured mean concentrations of total dissolved nitrogen and estimated recharge rates. The estimated nitrogen load before sewering was 1,675 pounds per year (lb/yr) and following sewering was 963 lb/yr. Mean concentrations of total dissolved nitrogen were assumed to have been reduced to 1.1 to 2.3 mg/L after the aquifer had stabilized and sewage-related nitrogen had been completely discharged from the system, with an estimated future load of 202 to 423 lb/yr. Nitrogen loads from groundwater discharge to the Niantic River Estuary from the lower part of the Niantic River watershed, including Pine Grove, were estimated to be 18,800 pounds (lb) in 2011. This compares with an additional 51,000 lb from the surface-water tributaries to the estuary and an unknown quantity of nitrogen load from stormwater runoff in the lower Niantic watershed.

Connecticut↗
USGS2016

Comparison of benthos and plankton for selected areas of concern and non-areas of concern in western Lake Michigan Rivers and Harbors in 2012

Recent data are lacking to assess whether impairments still exist at four of Wisconsin’s largest Lake Michigan harbors that were designated as Areas of Concern (AOCs) in the late 1980s due to sediment contamination and multiple Beneficial Use Impairments (BUIs), such as those affecting benthos (macroinvertebrates) and plankton (zooplankton and phytoplankton) communities. During three seasonal sampling events (“seasons”) in May through August 2012, the U.S. Geological Survey collected sediment benthos and water plankton at the four AOCs as well as six less-degraded non-AOCs along the western Lake Michigan shoreline to assess whether AOC communities were degraded in comparison to non-AOC communities. The four AOCs are the Lower Menominee River, the Lower Green Bay and Fox River, the Sheboygan River, and the Milwaukee Estuary. Due to their size and complexity, multiple locations or “subsites” were sampled within the Lower Green Bay and Fox River AOC (Lower Green Bay, the Fox River near Allouez, and the Fox River near De Pere) and within the Milwaukee Estuary AOC (the Milwaukee River, the Menomonee River, and the Milwaukee Harbor) and single locations were sampled at the other AOCs and non-AOCs. The six non-AOCs are the Escanaba River in Michigan, and the Oconto River, Ahnapee River, Kewaunee River, Manitowoc River, and Root River in Wisconsin. Benthos samples were collected by using Hester-Dendy artificial substrates deployed for 30 days and by using a dredge sampler; zooplankton were collected by net and phytoplankton by whole-water sampler. Except for the Lower Green Bay and Milwaukee Harbor locations, communities at each AOC were compared to all non-AOCs as a group and to paired non-AOCs using taxa relative abundances and metrics, including richness, diversity, and an Index of Biotic Integrity (IBI, for Hester-Dendy samples only). Benthos samples collected during one or more seasons were rated as degraded for at least one metric at all AOCs. In the Milwaukee Estuary, benthos richness was lower in the Milwaukee River subsite spring and summer samples and in the Menomonee River subsite spring sample relative to the paired non-AOCs. Benthos diversity and IBIs at the Menomonee River subsite and IBIs at the Milwaukee River subsite and Sheboygan River were significantly lower than at all non-AOCs as a group across all seasons and therefore were rated as degraded. In addition, IBIs at the Lower Menominee River were significantly lower than those at the paired non-AOCs during all seasons and were therefore rated degraded. Benthos at both Fox River subsites and the Milwaukee River subsite were significantly different from their paired non-AOCs during all three seasons, based on a comparison of the relative abundances of taxa using multivariate testing. Metrics for plankton at AOCs were not significantly lower than those at the paired or group non-AOCs during all seasons; however, zooplankton richness in spring at the Sheboygan River and in fall at the Menomonee River subsite was rated as degraded in comparison to paired non-AOCs. Also, zooplankton richness in fall at the Fox River near Allouez subsite and in spring at the Milwaukee River subsite was rated degraded overall because values were lower than at all non-AOCs as a group and lower than at the paired non-AOCs. Zooplankton diversity in fall at the Fox River near Allouez subsite and the Lower Menominee River was rated degraded in comparison to paired non-AOC comparison sites. Zooplankton communities at the Fox River near Allouez subsite were significantly different from the paired non-AOCs when multivariate comparisons were made without rotifers other than A. priodonta . Overall, benthos and zooplankton BUIs remained at the AOCs in 2012 but no AOCs with a phytoplankton BUI were rated degraded in comparison to non-AOCs. The use of a multiple ecological measures, structural and functional, and multiple statistical analyses, biological metrics and multivariate statistics, provided assessments that defined 2012 status of communities relative to less-impaired non-AOCs in the Great Lakes area.

Michigan↗
USGS2016

Flow characteristics and salinity patterns of tidal rivers within the northern Ten Thousand Islands, southwest Florida, water years 2007–14

Freshwater flow to the Ten Thousand Islands estuary has been altered by the construction of the Tamiami Trail and the Southern Golden Gate Estates. The Picayune Strand Restoration Project, which is associated with the Comprehensive Everglades Restoration Plan, has been implemented to improve freshwater delivery to the Ten Thousand Islands estuary by removing hundreds of miles of roads, emplacing hundreds of canal plugs, removing exotic vegetation, and constructing three pump stations. Quantifying the tributary flows and salinity patterns prior to, during, and after the restoration is essential to assessing the effectiveness of upstream restoration efforts. Tributary flow and salinity patterns during preliminary restoration efforts and prior to the installation of pump stations were analyzed to provide baseline data and preliminary analysis of changes due to restoration efforts. The study assessed streamflow and salinity data for water years 1 2007–2014 for the Faka Union River (canal flow included), East River, Little Wood River, Pumpkin River, and Blackwater River. Salinity data from the Palm River and Faka Union Boundary water-quality stations were also assessed. Faka Union River was the dominant contributor of freshwater during water years 2007–14 to the Ten Thousand Islands estuary, followed by Little Wood and East Rivers. Pumpkin River and Blackwater River were the least substantial contributors of freshwater flow. The lowest annual flow volumes, the highest annual mean salinities, and the highest percentage of salinity values greater than 35 parts per thousand (ppt) occurred in water year 2011 at all sites with available data, corresponding with the lowest annual rainfall during the study. The highest annual flow volumes and the lowest percentage of salinities greater than 35 ppt occurred in water year 2013 for all sites with available data, corresponding with the highest rainfall during the study. In water year 2014, the percentage of monitored annual flow contributed by East River increased and the percentage of flow contributed by Faka Union River decreased, compared to the earlier years. No changes in annual flow occurred at any sites west of Faka Union River. No changes in the relative flow contributions were observed during the wet season; however, the relative amounts of streamflow increased during the dry season at East River in 2014. East River had only 1 month of negative flow in 2014 compared to 6 months in 2011 and 7 months in 2008. Higher dry season flows in East River may be in response to restoration efforts. The sites to the west of Faka Union River had higher salinities on average than Faka Union River and East River. Faka Union River had the highest range in salinities, and Faka Union Boundary had the lowest range in salinities. Pumpkin River was the tributary with the lowest range in salinities. 1 Water year is defined as the 12-month period from October 1, for any given year, through September 30 of the following year.

Florida↗
USGS2000

Spatial distribution, temporal variability, and chemistry of the salt wedge in the lower Charles River, Massachusetts, June 1998 to July 1999

The Charles River is of great recreational and ecological value to the Boston metropolitan region and the Commonwealth of Massachusetts. It is also the focus of the U.S. Environmental Protection Agency (USEPA) Region I, Clean Charles 2005 Task Force. The main goal of the Task Force is to make the Charles River 'fishable and swimmable' by the year 2005. Achieving 'fishable and swimmable' conditions will require continued progress in addressing a range of environmental conditions now degrading water quality, including the infiltration of saltwater from Boston Harbor into the freshwater Charles River.To better understand the pattern of saltwater intrusion, the U.S. Geological Survey (USGS), in cooperation with the U.S. Environmental Protection Agency (USEPA), Massachusetts Department of Environmental Management (MADEM), and New England Interstate Water Pollution Control Commission (NEIWPCC), collected data on the spatial distribution, temporal variability, and chemistry of the saltwater that entered the lower Charles River from June 1998 to July 1999. The purpose of this investigation is to extend and complement a regional-scale study of Charles River water quality conducted in 1996 (T. Faber, U.S. Environmental Protection Agency, written commun., 1997), and the ongoing water monitoring activities of the Massachusetts Water Resources Authority (MWRA) and the Charles River Watershed Association (CRWA). The data collected by this investigation supports the Clean Charles 2005 Task Force by providing detailed information concerning a major factor limiting 'fishable and swimmable' conditions in the lower Charles River. Finally, the study will be used to assist current planning efforts of the Metropolitan District Commission (MDC) to restore the historic parklands of the lower Charles River.The 'Basin' is the local term for the reach of the Charles River that begins at the Watertown Dam in Watertown, Mass., and extends about 8 mi through suburban and urban areas to Boston Harbor. Discharge to the harbor is controlled by the 'new' Charles River Dam in Boston (fig. 1). The Basin was created by construction of the 'old' Charles River Dam in 1908 to solve Boston's sanitary problems. Prior to the building of the old Charles River Dam, the lower Charles River was a tidal estuary in which the water levels rose and fell twice daily with the tidal cycle. Low tide would expose untreated sewage that was discharged directly into the river. Exposed sewage created noxious odors and served as a breeding ground for mosquitoes that caused sporadic epidemics of malaria and yellow fever (Jobin, 1998). Damming of the river interrupted the normal tidal cycle and flooded the estuary by creating a freshwater pool (the Basin) that had a constant water elevation of about 0.8 meters (m) above mean sea level. Flooding of the estuary initially improved sanitary conditions and the Basin became a source of enjoyment for the local population and the focus of a large waterfront park in Boston and Cambridge (Jobin, 1998).Although the infiltration of saltwater from the harbor into the Basin was anticipated when the old Charles River Dam was built, neither the magnitude nor the consequences of the infiltration was considered. By 1975, the Metropolitan District Commission (MDC) determined that harbor water covered about 80 percent of the river bottom within the Basin and composed about 50 percent of its depth. The MDC also concluded that fish kills and odors in the spring of 1975 were likely the result of the sulfide-rich saltwater mixing with the overlying freshwater (Metropolitan District Commission, 1975).Saltwater from Boston Harbor that enters the Basin is known as the 'salt wedge' because of the shape it assumes as it moves upstream. Freshwater discharge from upstream pushes against the intruding harbor water until the density differences cause stratification to occur; the freshwater then overrides the denser harbor water (Fischer and others, 1979). The depth from

Water-Resources Investigations Report↗
USGS2003

A summary report of sediment processes in Chesapeake Bay and watershed

The Chesapeake Bay, the Nation's largest estuary, has been degraded because of diminished water quality, loss of habitat, and over-harvesting of living resources. Consequently, the bay was listed as an impaired water body due to excess nutrients and sediment. The Chesapeake Bay Program (CBP), a multi-jurisdictional partnership, completed an agreement called "Chesapeake 2000" that revises and establishes new restoration goals through 2010 in the bay and its watershed. The goal of this commitment is the removal of the bay from the list of impaired waterbodies by the year 2010. The CBP is committed to developing sediment and nutrient allocations for major basins within the bay watershed and to the process of examining new and innovative management plans in the estuary itself and along the coastal zones of the bay. However, additional information is required on the sources, transport, and deposition of sediment that affect water clarity. Because the information and data on sediment processes in the bay were not readily accessible to the CBP or to state, and local managers, a Sediment Workgroup (SWGP) was created in 2001. The primary objective of this report, therefore, is to provide a review of the literature on the sources, transport, and delivery of sediment in Chesapeake Bay and its watershed with discussion of potential implications for various management alternatives. The authors of the report have extracted, discussed, and summarized the important aspects of sediment and sedimentation that are most relevant to the CBP and other sediment related-issues with which resources managers are involved. This report summarizes the most relevant studies concerning sediment sources, transport and deposition in the watershed and estuary, sediments and relation to water clarity, and provides an extensive list of references for those wanting more information.

Water-Resources Investigations Report↗
USGS1993

Tidal and residual currents measured by an acoustic doppler current profiler at the west end of Carquinez Strait, San Francisco Bay, California, March to November 1988

Water-velocity profiles were collected at the west end of Carquinez Strait, San Francisco Bay, California, from March to November 1988, using an acoustic Doppler current profiler (ADCP). These data are a series of 10-minute-averaged water velocities collected at 1-meter vertical intervals (bins) in the 16.8-meter water column, beginning 2.1 meters above the estuary bed. To examine the vertical structure of the horizontal water velocities, the data are separated into individual time-series by bin and then used for time-series plots, harmonic analysis, and for input to digital filters. Three-dimensional graphic renditions of the filtered data are also used in the analysis. Harmonic analysis of the time-series data from each bin indicates that the dominant (12.42 hour or M2) partial tidal currents reverse direction near the bottom, on average, 20 minutes sooner than M2 partial tidal currents near the surface. Residual (nontidal) currents derived from the filtered data indicate that currents near the bottom are pre- dominantly up-estuary during the neap tides and down-estuary during the more energetic spring tides.

Water-Resources Investigations Report↗
USGS1965

Delaware River water quality Bristol to Marcus Hook, Pennsylvania, August 1949 to December 1963

During the 14-year period from August 1949 to July 1963, the U.S. Geological Survey, in cooperation with the city of Philadelphia, collected samples of river water once each month in the 43-mile reach of the Delaware River from Bristol to Marcus Hook, Pa., and daily at Trenton, 10 miles upstream from Bristol. This part of the Delaware is an estuary into which salt water is brought by tides; fresh water flows into the estuary at Trenton, NJ, and farther downstream from the Schuylkill River and other tributaries of the Delaware. In March, April, and May, when fresh-water flow is high, the average concentration of dissolved solids in the water at Bristol was 76 ppm (parts per million), and at Marcus Hook 112 PPM In August and September, streamflow is lower, and the average concentration of dissolved solids increased to 117 PPM at Bristol and 804 PPM at Marcus Hook. Major salinity invasions of the Delaware River occurred in 1949, 1953, 1954, 1957, and 1963. In each of these years the fresh-water flow into the tidal river at Trenton was low during the period from July to October. The greatest dissolved-solids concentrations in these monthly samples were 160 PPM at Bristol and 4,000 PPM at Marcus Hook. At times the dissolved-oxygen concentration of the river water has become dangerously low, especially in that reach of the river between Wharton Street and League Island. At the Benjamin Franklin Bridge, one-third of the samples of river water were less than 30 percent saturated with oxygen; however, no trend, either for better or for worse, was apparent during the 14-year period. It is useful now to summarize these monthly analyses for the period 1949-63 even though a much more detailed description of water quality in this reach of the estuary will soon become available through the use of recording instrumental conditions. This compendium of water-quality data is useful as an explicit statement of water quality during the 14-year study period and is valuable for directing attention to water-quality problems for selecting instrument sites, and for making comparative studies with the more detailed information which is already being obtained with the aid of recording instruments.

Water Supply Paper↗
USGS1997

Organic carbon balance and net ecosystem metabolism in Chesapeake Bay

The major fluxes of organic carbon associated with physical transport and biological metabolism were compiled, analyzed and compared for the mainstem portion of Chesapeake Bay (USA). In addition, 5 independent methods were used to calculate the annual mean net ecosystem metabolism (NEM = production - respiration) for the integrated Bay. These methods, which employed biogeochemical models, nutrient mass-balances anti summation of individual organic carbon fluxes, yielded remarkably similar estimates, with a mean NEM of +50 g C m-2 yr-1 (?? SE = 751, which is approximately 8% of the estimated annual average gross primary production. These calculations suggest a strong cross-sectional pattern in NEM throughout the Bay, wherein net heterotrophic metabolism prevails in the pelagic zones of the main channel, while net autotrophy occurs in the littoral zones which flank the deeper central area. For computational purposes, the estuary was separated into 3 regions along the land-sea gradient: (1) the oligohaline Upper Bay (11% of total area); (2) the mesohaline Mid Bay (36% of area); and (3) the polyhaline Lower Bay (53% of area). A distinct regional trend in NEM was observed along this salinity gradient, with net here(atrophy (NEM = 87 g C m-2 yr-1) in the Upper Bay, balanced metabolism in the Mid Bay and net autotrophy (NEM = +92 g C m-2 yr-1) in the Lower Bay. As a consequence of overall net autotrophy, the ratio of dissolved inorganic nitrogen (DIN) to total organic nitrogen (TON) changed from DIN:TON = 5.1 for riverine inputs to DIN:TON = 0.04 for water exported to the ocean. A striking feature of this organic C mass-balance was the relative dominance of biologically mediated metabolic fluxes compared to physical transport fluxes. The overall ratio of physical TOC inputs (1) to biotic primary production (P) was 0.08 for the whole estuary, but varied dramatically from 2.3 in the Upper Bay to 0.03 in the Mid and Lower Bay regions. Similarly, ecosystem respiration was some 6-fold higher than the sum of all physical carbon sinks. This general negative correspondence between I:P ratio and NEM, which occurred among Bay regions, was also evident in data available for organic C fluxes in other coastal ecosystems. An inverse relationship between NEM and P, postulated in a previous study, did not apply to Chesapeake Bay, and closer examination of available data revealed the importance of the loading ratio of DIN:TOC as a key control on coastal NEM. It is proposed here that the general global trend of coastal eutrophication will lead to increasing values of NEM in estuaries worldwide. The management implications of this trend are complex, involving both increased potential fisheries harvest and decreased demersal habitat.

Marine Ecology Progress Series↗
USGS2024

Variability in coastal habitat available for Longfin Smelt Spirinchus thaleichthys in the northeastern Pacific Ocean

An understanding of oceanographic conditions and processes important to marine animal ecology is fundamental to the development of effective management and conservation actions. Longfin Smelt ( Spirinchus thaleichthys ) is a pelagic forage fish found in coastal and estuarine waters along the Pacific coast of North America from Alaska to central California. Substantial population declines in California’s San Francisco Estuary, where Longfin Smelt are protected under California’s Endangered Species Act, have prompted extensive study of estuarine factors associated with the decline. However, coastal factors that affect up to two-thirds of the Longfin Smelt life cycle are poorly understood and may be important drivers of population dynamics. We compiled coastal observations from numerous sources to estimate the range-wide coastal marine distribution of Longfin Smelt and assess habitat factors affecting distribution in the northeast Pacific Ocean. Based on maximum entropy species distribution models, Longfin Smelt distribution was correlated with depth, distance from the nearest estuary, sea surface temperature, and sea surface chlorophyll. Longfin Smelt were found in shallow, higher productivity coastal waters closer to estuaries, with depth and temperature the most consistent factors influencing distribution. Habitat suitability was highly variable at the southern extent of the range, particularly off the California coast, and was largely driven by habitat contractions associated with warm-water conditions. Study results provide insights into the habitat and range-wide distribution of an at-risk estuarine-reliant forage fish and are the first step toward identifying processes that affect the marine portion of the Longfin Smelt life cycle.

Frontiers in Marine Science↗
USGS2022

Keeping an eye on water quality from the sky

You can learn a lot about rivers, lakes, estuaries, and oceans by looking down at them from the sky. Scientists use a technique called remote sensing to measure the amount of light or heat energy reflected and emitted from the Earth. Sensors can be on satellites or mounted on airplanes, helicopters, or drones. Scientists use this information to map the quality of water in the San Francisco Bay-Delta estuary. Remote sensing helps scientists see where and when there might be problems for human health or for the plants and animals living in the estuary.

California↗