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Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy

Executive Summary The Long Island South Shore Estuary Reserve Coordinated Water Resources Monitoring Strategy (CWRMS) provides an overview of the water-quality and ecological monitoring within the Reserve and presents suggestions from stakeholders for future data collection, data management, and coordination among monitoring programs. The South Shore Estuary Reserve, hereafter referred to as the Reserve, is a 173-square-mile network of bays and tributaries shaped by the south shore of Long Island (New York) and the barrier islands that was formed as a result of the last ice age (roughly 18,000 years ago). This overview and coordination document is based on information assembled from a series of meetings, a workshop, and individual correspondences with the CWRMS Project Advisory Committee, which was formed in 2015 to help guide the creation of the document, which reflects the current (2017) status of the Reserve and the need for additional data to address its water-quality issues and ecological health and to respond to a changing climate. The U.S. Geological Survey (USGS), in cooperation with the New York State Department of State Office of Planning, Development and Community Infrastructure and the South Shore Estuary Reserve Office, compiled information and recommendations to help stakeholders efficiently evaluate waters currently being monitored and address areas where necessary data are lacking. Water-quality monitoring in the Reserve is ongoing on the Federal, State, and local levels, and coordination among the various programs administered by the U.S. Environmental Protection Agency; National Oceanic and Atmospheric Administration; USGS; Shinnecock Tribal Nation; New York State; Nassau and Suffolk Counties; the Towns of Hempstead, Oyster Bay, Babylon, Islip, Brookhaven, and Southampton; and local universities and nonprofit organizations is necessary to ensure cooperation and efficient use of limited resources. Proper collection and archival of data are critical to the usability of data and methods—a sample of available repositories for monitoring data are provided in this report. Equally important are quality assurances of data and proper techniques of archival such that water and ecological data are collected and analyzed in a consistent manner, regardless of their sources, and that differences in methodologies are identified that might result in discrepancies in the compiled data. Details on monitoring programs, data gaps that are perceived by stakeholders and researchers in the area, and Project Advisory Committee recommendations are provided in this report to promote discussion and coordination. In most cases, resources to fill data gaps are needed, and the use of citizen science volunteers has been shown to help extend programs and provide insight into previously unaddressed areas of concern. This document, in conjunction with the CWRMS website and interactive mapper, is intended to inform the latest iteration of the Comprehensive Management Plan for the Reserve. Moreover, resource managers can use the CWRMS and mapper to identify areas of potential overlap and initiate conversations with stakeholders about addressing needs for additional monitoring of water quality and ecological health in the bays and tributaries of the Reserve.

New York

Forecasting selenium discharges to the San Francisco Bay-Delta Estuary: Ecological effects of a proposed San Luis Drain extension

Selenium discharges to the San Francisco Bay-Delta Estuary (Bay-Delta) could change significantly if federal and state agencies (1) approve an extension of the San Luis Drain to convey agricultural drainage from the western San Joaquin Valley to the North Bay (Suisun Bay, Carquinez Strait, and San Pablo Bay); (2) allow changes in flow patterns of the lower San Joaquin River and Bay-Delta while using an existing portion of the San Luis Drain to convey agricultural drainage to a tributary of the San Joaquin River; or (3) revise selenium criteria for the protection of aquatic life or issue criteria for the protection of wildlife. Understanding the biotransfer of selenium is essential to evaluating effects of selenium on Bay-Delta ecosystems. Confusion about selenium threats to fish and wildlife stem from (1) monitoring programs that do not address specific protocols necessary for an element that bioaccumulates; and (2) failure to consider the full complexity of the processes that result in selenium toxicity. Past studies show that predators are more at risk from selenium contamination than their prey, making it difficult to use traditional methods to predict risk from environmental concentrations alone. This report presents an approach to conceptualize and model the fate and effects of selenium under various load scenarios from the San Joaquin Valley. For each potential load, progressive forecasts show resulting (1) water-column concentration; (2) speciation; (3) transformation to particulate form; (4) particulate concentration; (5) bioaccumulation by invertebrates; (6) trophic transfer to predators; and (7) effects on those predators. Enough is known to establish a first-order understanding of relevant conditions, biological response, and ecological risks should selenium be discharged directly into the North Bay through a conveyance such as a proposed extension of the San Luis Drain. The approach presented here, the Bay-Delta selenium model, determines the mass, fate, and effects of selenium released to the Bay-Delta through use of (1) historical land-use, drainage, alluvial-fill, and runoff databases; (2) existing knowledge concerning biogeochemical reactions and physiological parameters of selenium (e.g., speciation, partitioning between dissolved and particulate forms, and bivalve assimilation efficiency); and (3) site-specific data mainly from 1986 to 1996 for clams and bottom-feeding fish and birds. Selenium load scenarios consider effluents from North Bay oil refineries and discharges of agricultural drainage from the San Joaquin Valley to enable calculation of (a) a composite freshwater endmember selenium concentration at the head of the estuary; and (b) a selenium concentration at a selected seawater location (Carquinez Strait) as a foundation for modeling. Analysis of selenium effects also takes into account the mode of conveyance for agricultural drainage (i.e., the San Luis Drain or San Joaquin River); and flows of the Sacramento River and San Joaquin River on a seasonal or monthly basis. Load scenarios for San Joaquin Valley mirror predictions made since 1955 of a worsening salt (and by inference, selenium) build-up exacerbated by an arid climate and massive irrigation. The reservoir of selenium in the San Joaquin Valley is sufficient to provide loading at an annual rate of approximately 42,500 pounds of selenium to a Bay-Delta disposal point for 63 to 304 years at the lower range of projections presented here, even if influx of selenium from the California Coast Ranges could be curtailed. Disposal of wastewaters on an annual basis outside of the San Joaquin Valley may slow the degradation of valley resources, but drainage alone cannot alleviate the salt and selenium build-up in the San Joaquin Valley, at least within a century. Load scenarios also show the different proportions of selenium loading to the Bay-Delta. Oil refinery loads from 1986 to 1992 ranged from 8.5 to 20 pounds of selenium per day; with treatment and cleanup, loads decreased to 3.0 pounds of selenium per day in 1999. In contrast, San Joaquin Valley agricultural drainage loads disposed of in a San Luis Drain extension could range from 45 to 117 pounds of selenium per day across a set of historical and future conditions. Components of this valley-wide load include five source subareas (i.e., Grassland, Westlands, Tulare, Kern, and Northern) defined by water and drainage management. Loads vary per subarea mainly because of proximity of the subarea to geologic sources of selenium and irrigation history. Loads from the Sacramento River, depending on flow conditions, range from 0.8 to 10 pounds of selenium per day. Loads from the San Joaquin River vary depending on restoration and flow conditions, which are considered. A consistent picture of ecological risk emerges under modeled selenium discharges from a proposed San Luis Drain extension. The threat to the estuary is greatest during low flow seasons and critically dry years. Where selenium undergoes reactions typical of low flow or longer residence time, highly problematic bioaccumulation in prey (food) is forecast. Surf scoter, greater and lesser scaup, and white sturgeon appear to be most at risk because these Bay-Delta predators feed on deposit and filter-feeding bivalves. Recent findings add Sacramento splittail and Dungeness crab to that list. During the low flow season of critically dry years, forecasted selenium concentrations in water, particulate matter, prey (diet), and predator tissue exceed guidelines with a high certainty of producing adverse effects under the most likely load scenario from a proposed San Luis Drain extension. High flows afford some protection under certain conditions in modeled San Joaquin River scenarios. However, meeting a combined goal of releasing a specific load during maximum flows and keeping selenium concentrations in the river below a certain objective to protect against bioaccumulation may not always be attainable. Management of the San Joaquin River on a constant concentration basis also could create problematic bioaccumulation during a wet year, especially during the low flow season, because high flows translate to high loads that are not always offset by seasonal river inflows. Prior to refinery cleanup, selenium contamination was sufficient to threaten reproduction in key species within the Bay-Delta ecosystems and human health advisories were posted based on selenium concentrations in tissues of diving ducks. During this time, selenium concentrations in the Bay-Delta were well below the most stringent recommended water quality criterion [1 microgram per liter (1 µg/L)]. Enhanced biogeochemical transformations to bioavailable particulate selenium and efficient bioaccumulation by bivalves characterized the system. If these biogeochemical conditions continue to prevail and agricultural selenium sources replace or exceed refinery sources, ecological forecasts suggest the risk of adverse effects will be difficult to eliminate under an out-of-valley resolution to the selenium problem. The Bay-Delta selenium model presented here is a systematic approach for conducting forecasts of the ecological effects from selenium on aquatic food webs. It is a new tool that links and models the major processes leading from loads through consumer organisms to predators. It also is a feasible approach for site-specific analysis and could provide a framework for developing new protective selenium foodweb guidelines and predator criteria. Model components that help ensure understanding ecosystems and the basis of environmental protection are (1) contaminant concentrations and speciation in sources, such as particulate material, that most influence bioavailability; (2) bioaccumulation models that calculate concentrations in diet, specifically in bivalves of the Bay-Delta that act as sensitive indicators of selenium contamination; (3) food-web type that determines what animals are threatened and when; and (4) multiple media concentrations (water, particulate material, and tissue of prey and predators) that, in-combination, determine risk or hazard.

California

Application of Acoustic and Optic Methods for Estimating Suspended-Solids Concentrations in the St. Lucie River Estuary, Florida

Acoustic and optic methods were applied to estimate suspended-solids concentrations in the St. Lucie River Estuary, southeastern Florida. Acoustic Doppler velocity meters were installed at the North Fork, Speedy Point, and Steele Point sites within the estuary. These sites provide varying flow, salinity, water-quality, and channel cross-sectional characteristics. The monitoring site at Steele Point was not used in the analyses because repeated instrument relocations (due to bridge construction) prevented a sufficient number of samples from being collected at the various locations. Acoustic and optic instruments were installed to collect water velocity, acoustic backscatter strength (ABS), and turbidity data that were used to assess the feasibility of estimating suspended-solids concentrations in the estuary. Other data collected at the monitoring sites include tidal stage, salinity, temperature, and periodic discharge measurements. Regression analyses were used to determine the relations of suspended-solids concentration to ABS and suspended-solids concentration to turbidity at the North Fork and Speedy Point sites. For samples used in regression analyses, measured suspended-solids concentrations at the North Fork and Speedy Point sites ranged from 3 to 37 milligrams per liter, and organic content ranged from 50 to 83 percent. Corresponding salinity for these samples ranged from 0.12 to 22.7 parts per thousand, and corresponding temperature ranged from 19.4 to 31.8 ?C. Relations determined using this technique are site specific and only describe suspended-solids concentrations at locations where data were collected. The suspended-solids concentration to ABS relation resulted in correlation coefficients of 0.78 and 0.63 at the North Fork and Speedy Point sites, respectively. The suspended-solids concentration to turbidity relation resulted in correlation coefficients of 0.73 and 0.89 at the North Fork and Speedy Point sites, respectively. The adequacy of the empirical equations seems to be limited by the number and distribution of suspended-solids samples collected throughout the expected concentration range at the North Fork and Speedy Point sites. Additionally, the ABS relations for both sites seem to overestimate at the low end and underestimate at the high end of the concentration range. Based on the sensitivity analysis, temperature had a greater effect than salinity on estimated suspended-solids concentrations. Temperature also appeared to affect ABS data, perhaps by changing the absorptive and reflective characteristics of the suspended material. Salinity and temperature had no observed effects on the turbidity relation at the North Fork and Speedy Point sites. Estimates of suspended-solids concentrations using ABS data were less 'erratic' than estimates using turbidity data. Combining ABS and turbidity data into one equation did not improve the accuracy of results, and therefore, was not considered.

Scientific Investigations Report

Vegetation of the Elwha River estuary: Chapter 8 in Coastal habitats of the Elwha River, Washington--biological and physical patterns and processes prior to dam removal

The Elwha River estuary supports one of the most diverse coastal wetland complexes yet described in the Salish Sea region, in terms of vegetation types and plant species richness. Using a combination of aerial imagery and vegetation plot sampling, we identified 6 primary vegetation types and 121 plant species in a 39.7 ha area. Most of the estuary is dominated by woody vegetation types, with mixed riparian forest being the most abundant (20 ha), followed by riparian shrub (6.3 ha) and willow-alder forest (3.9 ha). The shrub-emergent marsh transition vegetation type was fourth most abundant (2.2 ha), followed by minor amounts of dunegrass (1.75 ha) and emergent marsh (0.2 ha). This chapter documents the abundance, distribution, and floristics of these six vegetation types, including plant species richness, life form, species origin (native or introduced), and species wetland indicator status. These data will serve as a baseline to which future changes can be compared, following the impending removal of Glines Canyon and Elwha Dams upstream on the Elwha River. Dam removals may alter many of the processes, materials, and biotic interactions that influence the estuary plant communities, including hydrology, salinity, sediment and wood transport, nutrients, and plant-microbe interactions.

Washington

Effects of variations in flow characteristics through W.P. Franklin Lock and Dam on downstream water quality in the Caloosahatchee River Estuary and in McIntyre Creek in the J.N. “Ding” Darling National Wildlife Refuge, southern Florida, 2010–13

The U.S. Geological Survey studied water-quality trends at the mouth of McIntyre Creek, an entry point to the J.N. “Ding” Darling National Wildlife Refuge, to investigate correlations between flow rates and volumes through the W.P. Franklin Lock and Dam and water-quality constituents inside the refuge from March 2010 to December 2013. Outflow from Lake Okeechobee, and flows from Franklin Lock, tributaries to the Caloosahatchee River Estuary, and the Cape Coral canal system were examined to determine the sources and quantity of water to the study area. Salinity, temperature, dissolved-oxygen concentration, pH, turbidity, and chromophoric dissolved organic matter fluorescence (FDOM) were measured during moving-boat surveys and at a fixed location in McIntyre Creek. Chlorophyll fluorescence was also recorded in McIntyre Creek. Water-quality surveys were completed on 20 dates between 2011 and 2014 using moving-boat surveys. Franklin Lock contributed the majority of flow to the Caloosahatchee River. Between 2010 and 2013, the monthly mean flow rate at Franklin Lock ranged from 29 cubic feet per second in May 2011 to 10,650 cubic feet per second in August 2013. Instantaneous near-surface salinity in McIntyre Creek ranged from 12.9 parts per thousand on September 26, 2013, to 37.9 parts per thousand on June 27, 2011. Salinity in McIntyre Creek decreased with increasing flow rate through Franklin Lock. Flow rates through Franklin Lock explained 61 percent of the variation in salinity in McIntyre Creek. Salinity data from moving-boat surveys also indicate that an increase in flow rate at Franklin Lock decreases salinity in the Caloosahatchee River Estuary, and a reduction or elimination in flow increases salinity. The FDOM in McIntyre Creek was positively correlated with flow at Franklin Lock, and 54 percent of the variation in FDOM can be attributed to the flow rate through Franklin Lock. Data from moving-boat surveys indicate that FDOM increases when flow volume from Franklin Lock increases. The highest FDOM recorded during a survey was at Billy’s Creek. Chlorophyll fluorescence was positively correlated with flow at Franklin Lock, with 23 percent of the variation explained by the flow rate at Franklin Lock. An increase in flow rate at Franklin Lock resulted in a decrease in pH (21 percent of variation explained by flow rates). Data from the pH surveys indicate an increase in pH with distance from Franklin Lock. Turbidity and dissolved oxygen near the surface in McIntyre Creek were not correlated with flow rate at Franklin Lock. Moving-boat surveys did not document a change in turbidity or dissolved oxygen with a change in distance from the Franklin Lock. Correlations between Franklin Lock flow rate and water quality in McIntyre Creek indicate that releases at Franklin Lock affect water quality in the Caloosahatchee River Estuary and Ding Darling Refuge.

Florida

Geochemical conditions and nitrogen transport in nearshore groundwater and the subterranean estuary at a Cape Cod embayment, East Falmouth, Massachusetts, 2013–14

Nitrogen transport and transformation were studied during 2013 to 2014 by the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency, in a subterranean estuary beneath onshore locations on the Seacoast Shores peninsula, a residential area in Falmouth, Massachusetts, served by septic systems and cesspools, and adjacent offshore locations in the Eel River, a saltwater embayment connected to the ocean. The field investigation included installation and sampling of clusters of wells and temporary sampling points near a transect extending from about 35 meters (m) onshore to 18 m offshore. The fresh groundwater at the study site formed a lens about 11 m thick at the shoreline that was underlain by saline groundwater. Groundwater flow in the water-table aquifer was oriented northwestward toward the embayment. Nitrate concentrations in the fresh groundwater at a site about 35 m onshore increased in the downward direction from less than 500 micromoles per liter near the water table to about 1,700 micromoles per liter just above the freshwater/saltwater transition zone. Dissolved oxygen was largely absent in the onshore fresh groundwater. Distributions of salinity, dissolved oxygen, and nitrate at the shoreline and offshore generally were similar to those onshore; at some locations, however, shallow saline water was present above the freshwater, and there were scattered occurrences of elevated dissolved oxygen concentrations. Geochemical indicators of nitrate reduction, including concentrations of the reaction product nitrogen gas, stable isotope ratios of nitrate and nitrogen gas, and changes in alkalinity, provided evidence for nitrate reduction in two zones separated vertically by a zone 7–8 m thick with no evidence of nitrate reduction. The shallow nitrate-reduction zone was near the water table in fresh groundwater onshore, where nitrate reduction may be related to particular recharge conditions at nearby sources. The shallow nitrate-reduction zone also may be related to an interval of fine-grained sediments at about the same altitude (−1 to −6 m relative to the National Geodetic Vertical Datum of 1929), where flow is slower and reactive electron donors such as solid organic carbon, iron, or sulfide phases may be present to drive the reduction. The deep nitrate-reduction zone was near the freshwater/saltwater transition zone, where nitrate reduction may be related to mixing of freshwater containing nitrate and saltwater containing dissolved organic carbon and ammonium, or to fine-grained sediments near the transition zone. The maximum amount of nitrate converted to nitrogen gas was estimated to be less than or equal to 300 micromoles per liter in both nitrate-reduction zones. The presence of nitrate and low dissolved oxygen concentrations in the 7–8-meter-thick zone between the shallow and deep nitrate-reduction zones are conditions that could permit nitrate reduction. The absence of evidence of nitrate reduction in the high-nitrate zone may have resulted from the lack of reactive electron donors in that depth interval. The high-nitrate zone dissipated somewhat in the offshore direction, but the current study did not extend far enough to encompass the fresh groundwater discharge area or determine how much of the nitrate was removed prior to discharge. A shallow intertidal saltwater cell was formed during a spring tide by saltwater infiltration during tidal run-up on the beach. Nitrate reduction might have occurred if nitrate-containing fresh groundwater discharging to the estuary mixed with the saltwater containing dissolved organic carbon in this zone, but samples collected from the intertidal saltwater cell during this study were not analyzed for indicators of nitrate reduction. Elevated dissolved oxygen concentrations in fresh groundwater 9 m offshore may indicate that groundwater flow was partly oblique to the sampling transect or that groundwater from a regional flow system was converging under the river near the study area. Flow directions also may have been affected by aquifer heterogeneity such as the shallow fine-grained sediments onshore and at the bottom of the Eel River. Improved understanding of the fate of nitrate in this type of complex setting might be gained by including additional characterization of aquifer heterogeneity and groundwater flow and extending investigations of nitrate reduction to the shallow sediments in the intertidal saltwater cell and adjacent subtidal zone and to locations farther offshore beneath the estuary.

Massachusetts

Physical, Hydrological, and Biological Characteristics of the Loxahatchee River Estuary, Florida

The Loxahatchee River estuary empties into the Atlantic Ocean at Jupiter Inlet in southeastern Florida. Although relatively small, the estuary is important for its esthetic value and for its sport fishing, boating, recreation, tourism, and prime residential development. In recent years, the condition of the estuary has become of concern to many citizens and agencies of the State. In response to this concern, the U.S. Geological Survey planned and carried out an in-depth environmental investigation. The events that led to the investigation and the objectives of the investigation are outlined in a recent U.S. Geological Survey report by McPherson and Sabanskas (WRI 80-1109).

Water-Resources Investigations Report

Sediment concentrations and loads in the Loxahatchee River estuary, Florida, 1980-82

This study was conducted to estimate the magnitude of sediment loads and the general spatial and temporal patterns of sediment transport in the Loxahatchee River estuary, Florida. Mean concentrations of suspended sediment generally were higher in the Jupiter Inlet area than in the remainder of the embayment area. Concentrations of suspended sediment varied with season and weather conditions. Concentrations in selected tributaries following Tropical Storm Dennis in August 1981 immediately increased as much as 16 times over concentrations before the storm. Suspended-sediment loads from the tributaries were also highly seasonal and storm related. During a 61-day period of above-average rainfall that included Tropical Storm Dennis, 5 major tributaries discharged 926 tons (short) of suspended sediment to the estuary, accounting for 74 percent of the input for the 1981 water year and 49 percent of the input for the 20-month study period. Suspended-sediment loads at Jupiter Inlet and at the mouth of the estuary embayment on both incoming and outgoing tides far exceeded tributary loads, but the direction of long-term, net tidal transport was not determined. (USGS)

Water-Resources Investigations Report

Determination of mass balance and entrainment in the stratified Duwamish River Estuary, King County, Washington

During a study of the effects of waste-water input on the stratified Duwamish River estuary, intensive water-velocity and salinity measurements were made in both the lower salt wedge and the upper fresher water layer for tidal-cycle periods. The net movement of water and salt mass past a cross section during a tidal cycle was determined from integration of the measured rates of movement of water and salt past the section. The net volume of water that moved downstream past the section during the cycle agreed with the volume of fresh-water inflow at the head of the estuary within (1) 3.8 and 7.2 percent, respectively, for two studies made during periods of maximum and minimum tidal-prism thickness and identical inflow rates .of 312 cfs (cubic feet per second), and (2) 15 percent for one study made during a period of average tidal-prism thickness and an inflow rate of 1,280 cfs. For the three studies, the difference between salt mass transported upstream and downstream during the cycles ranged from 0.8 to 19 percent of the respective mean salt-mass transport. Water was entrained from the .salt-water wedge into the overlying layer of mixed fresh and salt water at tidal-cycle-average rates of 30 and 69 cfs per million square feet of interface for the inflow rates of 312 cfs, and 99 cfs per million square feet of interface for an inflow rate of 1,280 cfs. At a constant inflow rate, the rate of entrainment of salt-wedge water in the Duwamish River estuary more than doubled for a doubling of tidal-prism thickness. It also doubled for a quadrupling of inflow rate at about constant tidal-prism thickness.

Water Supply Paper

Processes governing phytoplankton blooms in estuaries. I: The local production-loss balance

The formation and spatial distribution of phytoplankton blooms in estuaries are controlled by (1) local mechanisms, which determine the production-loss balance for a water column at a particular spatial location (i.e. control if a bloom is possible), and (2) transport-related mechanisms, which govern biomass distribution (i.e. control if and where a bloom actually occurs). In this study, the first of a 2-paper series, we use a depth-averaged numerical model as a theoretical tool to describe how interacting local conditions (water column height, light availability, benthic grazing) influence the local balance between phytoplankton sources and sinks. We also explore trends in the spatial variability of the production-loss balance across the topographic gradients between deep channels and lateral shoals which are characteristic of shallow estuaries. For example, under conditions of high turbidity and slow benthic grazing the highest rates of phytoplankton population growth are found in the shallowest regions. On the other hand, with low turbidity and rapid benthic grazing the highest growth rates occur in the deeper areas. We also explore the effects of semidiurnal tidal variation in water column height, as well as spring-neap variability. Local population growth in the shallowest regions is very sensitive to tidal-scale shallowing and deepening of the water column, especially in the presence of benthic grazing. A spring-neap signal in population growth rate is also prominent in the shallow areas. Population growth in deeper regions is less sensitive to temporal variations in tidal elevation. These results show that both shallow and deep regions of estuaries can act as sources or sinks for phytoplankton biomass, depending on the local conditions of mean water column height, tidal amplitude, light-limited growth rate, and consumption by grazers.

Marine Ecology Progress Series

Sediment DIN fluxes and preferential recycling of benthic microalgal nitrogen in a shallow macrotidal estuary

Sediment -water fluxes of NH 4 + , NO 3 - , dissolved inorganic carbon, and O 2 were measured in cores collected from the upper Rowley River estuary , Massachusetts, and used to calculate rates of organic nitrogen (N) mineralization, nitrification, and coupled and direct denitrification (DNF). The cores contained 15 N label in benthic microalgae (BMA) and in NO 3 - in the overlying water as a result of an ongoing whole- estuary 15 NO 3 - enrichment study (NISOTREX II). The tracer allowed for estimation of gross NO 3 - regeneration in sediments and the contribution of BMA derived N to total mineralization. The mean mineralization rate between sites was 16.0 ± 2.0 mmol N m -2 d -1 . Approximately 13 to 56% of the mineralized N was nitrified at rates ranging from 1.8 to 10.1 mmol N m -2 d -1 . Total denitrification was dominated by direct DNF (3.6 mmol N m -2 d -1 ) furthest upstream, where NO 3 - concentrations were highest. Coupled DNF was most important (8.0 mmol N m -2 d -1 ) in the sediments with high nitrification and low water column NO 3 - . A gross NO 3 - flux from sediments to water of 0.9 to 2.1 mmol N m -2 d -1 was estimated from the isotope dilution of δ 15 NO 3 - in the overlying water of the cores. The isotope dilution seen in the cores was also detected as a deviation from conservative δ 15 NO 3 - mixing along estuarine transects. Incorporation of this NO 3 - regeneration into the DNF calculations effectively increased the estimate of direct DNF by up to 50% and decreased the coupled DNF estimate by up to 220%. Increasing δ 15 NH 4 + in the water of the cores indicated that the 15 N-labelled BMA were preferentially mineralized over bulk sediment organic N. Additional 15 N enrichments in the sediment bacterial biomarker diaminopimelic acid showed a link among 15 N-labeled BMA, active bacteria, and 15 NH 4 + released to the overlying water. Based on δ 15 NH 4 + enrichments in the cores, BMA accounted for approximately 50 to 100% of the N mineralized. An isotopic enrichment of δ 15 NH 4 + above background in the estuary was observed at a magnitude consistent with the core-based rates of BMA mineralization. These results provide further evidence that BMA are not unidirectional sinks for water column-dissolved organic nitrogen , but instead act to turn over N between sediments and estuarine water on the scale of days.

Marine Ecology Progress Series

Stress gradients structure spatial variability in coastal tidal marsh plant composition and diversity in a major Pacific coast estuary

Understanding the drivers of variability in plant diversity from local to landscape spatial scales is a challenge in ecological systems. Environmental gradients exist at several spatial scales and can be nested hierarchically, influencing patterns of plant diversity in complex ways. As plant community dynamics influence ecosystem function, understanding the drivers of plant community variability across space is paramount for predicting potential shifts in ecosystem function from global change. Determining the scales at which stress gradients influence vegetation composition is crucial to inform management and restoration of tidal marshes for specific functions. Here, we analyzed vegetation community composition in 51 tidal marshes from the San Francisco Bay Estuary, California, USA. We used model-based compositional analysis and rank abundance curves to quantify environmental (elevation/tidal frame position, distance to channel, and channel salinity) and species trait (species form, wetland indicator status, and native status) influences on plant community variability at the marsh site and estuary scales. While environmental impacts on plant diversity varied by species and their relationships to each other, overall impacts increased in strength from marsh to estuary scales. Relative species abundance was important in structuring these tidal marsh communities even with the limited species pools dominated by a few species. Rank abundance curves revealed different community structures by region with higher species evenness at plots higher in the tidal frame and adjacent to freshwater channels. By identifying interactions (species–species, species–environment, and environment–trait) at multiple scales (local, landscape), we begin to understand how variability measurements could be interpreted for conservation and land management decisions.

California

Recent nitrogen storage and accumulation rates in mangrove soils exceed historic rates in the urbanized San Juan Bay Estuary (Puerto Rico, United States)

Tropical mangrove forests have been described as “coastal kidneys,” promoting sediment deposition and filtering contaminants, including excess nutrients. Coastal areas throughout the world are experiencing increased human activities, resulting in altered geomorphology, hydrology, and nutrient inputs. To effectively manage and sustain coastal mangroves, it is important to understand nitrogen (N) storage and accumulation in systems where human activities are causing rapid changes in N inputs and cycling. We examined N storage and accumulation rates in recent (1970 – 2016) and historic (1930 – 1970) decades in the context of urbanization in the San Juan Bay Estuary (SJBE, Puerto Rico), using mangrove soil cores that were radiometrically dated. Local anthropogenic stressors can alter N storage rates in peri-urban mangrove systems either directly by increasing N soil fertility or indirectly by altering hydrology (e.g., dredging, filling, and canalization). Nitrogen accumulation rates were greater in recent decades than historic decades at Piñones Forest and Martin Peña East. Martin Peña East was characterized by high urbanization, and Piñones, by the least urbanization in the SJBE. The mangrove forest at Martin Peña East fringed a poorly drained canal and often received raw sewage inputs, with N accumulation rates ranging from 17.7 to 37.9 g m –2 y –1 in recent decades. The Piñones Forest was isolated and had low flushing, possibly exacerbated by river damming, with N accumulation rates ranging from 18.6 to 24.2 g m –2 y –1 in recent decades. Nearly all (96.3%) of the estuary-wide mangrove N (9.4 Mg ha –1 ) was stored in the soils with 7.1 Mg ha –1 sequestered during 1970–2017 (0–18 cm) and 2.3 Mg ha –1 during 1930–1970 (19–28 cm). Estuary-wide mangrove soil N accumulation rates were over twice as great in recent decades (0.18 ± 0.002 Mg ha –1 y –1 ) than historically (0.08 ± 0.001 Mg ha –1 y –1 ). Nitrogen accumulation rates in SJBE mangrove soils in recent times were twofold larger than the rate of human-consumed food N that is exported as wastewater (0.08 Mg ha –1 y –1 ), suggesting the potential for mangroves to sequester human-derived N. Conservation and effective management of mangrove forests and their surrounding watersheds in the Anthropocene are important for maintaining water quality in coastal communities throughout tropical regions.

Puerto Rico, San Juan Bay Estuary

Simulated estuary-wide response of seagrass (Zostera marina) to future scenarios of temperature and sea level

Seagrass communities are a vital component of estuarine ecosystems, but are threatened by projected sea level rise (SLR) and temperature increases with climate change. To understand these potential effects, we developed a spatially explicit model that represents seagrass ( Zostera marina ) habitat and estuary-wide productivity for Barnegat Bay-Little Egg Harbor (BB-LEH) in New Jersey, United States. Our modeling approach included an offline coupling of a numerical seagrass biomass model with the spatially variable environmental conditions from a hydrodynamic model to calculate above and belowground biomass at each grid cell of the hydrodynamic model domain. Once calibrated to represent present day seagrass habitat and estuary-wide annual productivity, we applied combinations of increasing air temperature and sea level following regionally specific climate change projections, enabling analysis of the individual and combined impacts of these variables on seagrass biomass and spatial coverage. Under the SLR scenarios, the current model domain boundaries were maintained, as the land surrounding BB-LEH is unlikely to shift significantly in the future. SLR caused habitat extent to decrease dramatically, pushing seagrass beds toward the coastline with increasing depth, with a 100% loss of habitat by the maximum SLR scenario. The dramatic loss of seagrass habitat under SLR was in part due to the assumption that surrounding land would not be inundated, as the model did not allow for habitat expansion outside the current boundaries of the bay. Temperature increases slightly elevated the rate of summer die-off and decreased habitat area only under the highest temperature increase scenarios. In combined scenarios, the effects of SLR far outweighed the effects of temperature increase. Sensitivity analysis of the model revealed the greatest sensitivity to changes in parameters affecting light limitation and seagrass mortality, but no sensitivity to changes in nutrient limitation constants. The high vulnerability of seagrass in the bay to SLR exceeded that demonstrated for other systems, highlighting the importance of site- and region-specific assessments of estuaries under climate change.

New Jersey

Nutrient and carbonate chemistry patterns associated with Karenia brevis blooms in three West Florida Shelf estuaries 2020-2023

Ocean acidification (OA) driven by eutrophication, riverine discharge, and other threats from local population growth that affect the inorganic carbonate system is already affecting the eastern Gulf of Mexico. Long-term declines in pH of ~ -0.001 pH units yr -1 have been observed in many southwest Florida estuaries over the past few decades. Coastal and estuarine waters of southwest Florida experience high biomass harmful algal blooms (HABs) of the dinoflagellate Karenia brevis nearly every year; and these blooms have the potential to impact and be impacted by seasonal to interannual patterns of carbonate chemistry. Sampling was conducted seasonally along three estuarine transects (Tampa Bay, Charlotte Harbor, Caloosahatchee River) between May 2020 and May 2023 to obtain baseline measurements of carbonate chemistry prior to, during, and following K. brevis blooms. Conductivity, temperature and depth data and discrete water samples for K. brevis cell abundance, nutrients, and carbonate chemistry (total alkalinity, dissolved inorganic carbonate (DIC), p CO 2, and pH T were evaluated to identify seasonal patterns and linkages among carbonate system variables, nutrients, and K. brevis blooms. Karenia brevis blooms were observed during six samplings, and highest p CO 2 and lowest pH T was observed either during or after blooms in all three estuaries. Highest average pH and lowest p CO 2 were observed in Tampa Bay. In all three estuaries, average DIC and pH T were higher and p CO 2 was lower during dry seasons than wet seasons. There was strong influence of net community calcification (NCC) and net community production (NCP) on the carbonate system; and NCC : NCP ratios in Tampa Bay, Charlotte Harbor, and the Caloosahatchee River were 0.83, 0.93, and 1.02, respectively. Linear relationships between salinity and dissolved ammonium, phosphate, and nitrate indicate strong influence of freshwater inflow from river input and discharge events on nutrient concentrations. This study is a first step towards connecting observations of high biomass blooms like those caused by K. brevis and alterations of carbonate chemistry in Southwest Florida. Our study demonstrates the need for integrated monitoring to improve understanding of interactions among the carbonate system, HABs, water quality, and acidification over local to regional spatial scales and event to decadal time scales.

Florida

Social foraging and feeding environment of the black-crowned night heron in an industrialized estuary

A nesting colony of more than 300 pairs of Black-crowned Night-Herons in the Patapsco River estuary, Baltimore Harber, Maryland was monitored from May to July 1988. The departure direction and departure time of each Heron was recorded during mornjng and evening observations at the colony. In addition, individual Herons were followed to landing sites in the estuary with small boats and aircraft. Herons appear to be quite social in foraging and may concentrate their feeding in some of the most industrialized parts of the estuary. Night-Herons may prosper in urban environments because some of their prey are attracted to intense shoreline illumination at night. New quantitative methods were developed to cope with the lack of statistical independence when dealing with social species.

Maryland

Using mollusks as indicators of restoration in nearshore zones of south Florida's estuaries

Current south Florida ecosystem restoration efforts are focused on restoring more natural freshwater flow through the wetlands and into the estuaries to reestablish natural salinity gradients, particularly in the nearshore zones. Indicator taxa are used to monitor and assess restoration progress and the current suite of biota used for the estuaries in south Florida (Biscayne Bay, Florida Bay, and the southwest mangrove riverine system) does not include mollusks. Mollusks make excellent indicators because they are found in all south Florida environments, are relatively stationary in postlarval stages, and, therefore, do not leave a site when conditions change. Their hard shells increase the likelihood of preservation after death, thus, making it possible to assess death assemblages. In addition to these features, many mollusks can be quickly sampled in the field and assessed in the lab, so poor visibility and tidal cycles are not an issue for monitoring surveys. Here we examine 27 years of molluscan data from 887 samples from 640 visits to 167 sites in south Florida's estuaries and present a suite of taxa that could be used as indicators for restoration of the oligohaline to mesohaline (0.5 to 17.9 psu) nearshore zones. Cyrenoida floridana , Hydrobiidae, Polymesoda caroliniana , Crassostrea virginica , and additional taxa are included with suggested sampling strategies.

Florida

Tidal Wetlands and Estuaries

1. The top 1 m of tidal wetland soils and estuarine sediments of North America contains 1,886 ± 1046 teragrams of carbon (Tg C). [High confidence, Very likely] 2. Soil carbon accumulation rate (i.e., sediment burial) in North American tidal wetlands is currently 9 ± 5 Tg C per year and estuarine carbon burial is 5 ± 3 Tg C per year. [High confidence, Likely] 3. The lateral flux of carbon from tidal wetlands to estuaries is 16 ± 10 Tg C per year for North America. [Low confidence, Likely] 4. In North America, tidal wetlands remove 27 ± 13 Tg C per year from the atmosphere, estuaries outgas 10 ± 10 Tg C per year to the atmosphere, and the net uptake by the combined wetland-estuary system is 17 ± 16 Tg C per year. [Low confidence, Likely] 5. Research and modeling needs are greatest for understanding responses to accelerated sea level rise, mapping tidal wetland and estuarine extent and quantification of CO2 and CH4 exchange with the atmosphere, especially in large, under-sampled, and rapidly changing regions. [High confidence, Likely] Note: Confidence levels are provided as appropriate for quantitative, but not qualitative, Key Findings and statements.

Book chapter