The National Estuarine Research Reserve System (NERRS), consisting of a network of 26 protected estuarine reserves in the conterminous US, Alaska, and Puerto Rico, generates comprehensive research and monitoring databases in support of coastal resource-management programs. Integrated water-quality, nutrient, and biological monitoring protocols conducted by the NERRS program have been valuable for identifying and tracking short-term variability and long-term changes in the integrity and biodiversity of estuarine systems nationwide. Four areas of biological monitoring in the NERRS program form the foundation for detailed research initiatives; these include (1) submerged aquatic vegetation (SAV) and emergent vegetation (marsh plants), (2) benthos (benthic invertebrates and benthic algae), (3) plankton (specifically larvae), and (4) nekton (fish, decapod crustaceans, and other swimming animals). Watershed and land-use/land-cover characterizations, benthic habitat mapping, and benthic community surveys comprise other high-priority initiatives of the NERRS program. The articles in this volume provide results of both system-wide investigations and site-specific case studies of the NERRS research and monitoring initiatives.

Environmental monitoring is both a scientific and management imperative for effective coastal and estuarine resources research, management, and education. The establishment of monitoring programs provides for baseline studies, trend analyses, and impact assessments as related to both short-term variability and long-term change within estuarine environments. The effectiveness of these programs is dependent not only on the data collection but also on the implementation and maintenance of procedures to ensure access to high-quality data, data documentation, and derived products. Advances in information technology are improving the way resource managers and researchers can assimilate, manage, disseminate, and share environmental data and information. The Integrated Ocean Observing System (IOOS) initiative is developing an integrated national system for the United States' coastal zone built upon federal monitoring efforts and regional coastal observing systems that monitor the state and variability of the coastal waters and estuaries of the United States. The National Oceanic and Atmospheric Administration's (NOAA) National Estuarine Research Reserve System (NERRS) acknowledges the importance of long-term environmental monitoring programs and data and information dissemination via the NERRS System-Wide Monitoring Program (SWMP). Consistent with the IOOS initiative and in support of sound data-management and -dissemination practices, the NERRS SWMP has implemented and sustains procedures to manage the basic infrastructure and data protocol to support the assimilation and exchange of quality-controlled data, metadata, and information within the framework of NERRS sites, state coastal zone management programs, and NOAA/OCRM as well as other state and federally funded education, monitoring, and research programs.

Shallow estuarine habitats are normally characterized by wide interannual and intraannual fluctuations in water-quality variables, including dissolved oxygen; however, the short-term variability in water-quality variables is seldom measured and characterized. Water-quality data collected semicontinuously by automated data sondes from 1995 to 2000 at 55 sites among 22 National Estuarine Research Reserves (NERR) were analyzed to characterize temporal variability and compare conditions among estuarine systems and regions. Three-way analysis of variance (ANOVA) models revealed several significant interannual and seasonal differences for water-quality variables for many sites sampled within a reserve; however, interannual trends with respect to reserve or region were not readily apparent. Salinity and hypoxic events (dissolved oxygen [DO] < 28% saturation [sat]) were generally greatest in summer or fall. Evapotranspiration and precipitation appeared to influence seasonal salinity patterns at reserve sites. Abrupt short-term decreases and sustained long-term decreases in salinity associated with precipitation events were documented during the passage of tropical systems. An abrupt decrease in water temperature prior to storm passage was noted, with increasing cooling effects related to increasing storm intensity. Although hypoxia occurred over a broad geographic range, it was primarily experienced at sites with sustained warm water conditions. Hypoxia was strongly influenced by latitude and climate. Duration of hypoxia at most reserves persisted less than 12 hours. Increased deployment duration was shown to increase the percentage of time with hypoxic conditions (DO < 28% sat) and decrease the percentage of time with supersaturation (DO > 120% sat) at many sites. The large fluctuations in dissolved oxygen that occur over short time periods in estuaries demonstrate the need for long-term continuous measurements to estimate the frequency and duration of exposure to low DO. Without continuous monitoring, many low-DO events would have been missed, thus underestimating the potential impacts from this type of water-quality variability. The synthesis of water-quality data from the NERR sites indicates that reserves have not experienced many of the problems found in other more populated locales.

Time-series observations and point measurements were used to assess seasonal patterns, tidal cycle variations, and the impact of major forcings on salinity, water temperature, turbidity, suspended sediments, and dissolved nutrients in the Webhannet River estuary (Wells National Estuarine Research Reserve). Because of the small size of the Webhannet River watershed, the main tributary of the estuary responds quickly to precipitation events, resulting in rapid increases in freshwater inputs, large decreases in salinity, and increases in suspended sediments and turbidity. Overall, suspended sediment concentrations were typically highest in the upper estuary and lowest in the Webhannet River, averaging 17.2 mg/L and 3.4 mg/L, respectively. The dissolved nutrient concentrations were variable; however, several species showed spatial and temporal patterns. Similar to suspended sediments, ammonium concentrations were typically highest in the upper estuary and lowest in the Webhannet River, averaging 4.60 μM and 1.01 μM, respectively. Average dissolved silica and nitrate plus nitrite concentrations were typically highest in the Webhannet River (32.96 and 5.13 μM, respectively) and the upper estuary (30.09 and 3.66 μM, respectively). Average orthophosphate concentrations decreased up-estuary from 0.56 μM near the mouth to 0.08 μM in the Webhannet River.

The impacts of major storms were observed during Hurricane Bob in August 1991 and Tropical Storm Floyd in September 1999. As a result of the passage of Hurricane Bob, approximately 13.49 cm of rain fell in the watershed. The instantaneous peak discharge of the Webhannet River reached 15.9 m³/s (compared with a long-term average of ∼0.5 m³/s), causing the salinity to decrease to 0.1 psu in the upper estuary and to ∼7.0 psu in the lower estuary. The suspended sediment concentrations reached 34.6 mg/L in the upper estuary. The major decrease in salinity in the lower estuary as a result of Hurricane Bob was especially noteworthy because of the significant influence of oceanic inputs. Also notable was how rapid the salinities returned to prehurricane levels at high tide (within a few tidal cycles). Conversely, minimum daily salinities, which occurred at low tide, took over 10 days to rebound to prehurricane levels. Consequently, very large fluctuations in salinity and turbidity occurred over short time scales. Other heavy precipitation events during low-discharge conditions also increased turbidity and suspended sediment concentrations by eroding the adjacent salt marshes and tidal flats.

Estuaries integrate atmospheric, watershed, oceanic, and human influences over space and time. Therefore, spatial and temporal patterns in estuarine water-column properties are useful as metrics to evaluate external factors related to internal processes. The National Estuarine Research Reserve monitoring program, including the North Inlet–Winyah Bay complex in South Carolina, provides an ideal setting to track water quality relationships. Our goal was to assess hydrography, chlorophyll a, and particulate and dissolved materials from monitoring data collected at sites from both the salt and estuarine marsh components since 1993–94. Salinity, turbidity, dissolved organic carbon, suspended solids, and chlorophyll a were much greater at the estuarine site, whereas organic nitrogen dominated the total nitrogen pool at both locations. Nitrate was a significant fraction of the total nitrogen pool at the estuarine site but not within the salt marsh. Whereas dissolved organic nitrogen was positively correlated to water temperature, nitrate concentrations were the lowest in the summer. Principal components analysis identified seasonal patterns within the salt marsh for temperature, chlorophyll a, ammonium, suspended solids, and particulate nitrogen. These parameters, grouped together as a primary component, were positively correlated to Spartina alterniflora biomass. In contrast, the estuarine site was more characterized by salinity, pH, and dissolved organic carbon. Although the water-column properties of the salt marsh site reflected a high degree of internal production and remineralization in the summer, patterns at the estuarine site were more likely influenced by seasonal changes in circulation and biogeochemical processing common to coastal plain estuaries.

Nonparametric harmonic analysis, a new data-analytic method for deconvoluting and graphically presenting the periodic signals in water quality time-series data, is demonstrated using data from the System-Wide Monitoring Program (SWMP) of the Sapelo Island National Estuarine Research Reserve (Georgia). The analysis uses the new statistical technology known as generalized additive models, an alternative to the classical harmonic regression analysis used for centuries to model and predict tidal forcing. Generalized additive models are especially well-suited for data-rich settings in which strong and nonsinusoidal periodic signals are expected. Data from two sampling sites on Sapelo Island, Georgia, show strong and regular M₂–dominated periodicities in water depth. At the Hunt Dock (HD) site, water temperature, pH, and dissolved oxygen (DO) have strong diel signatures in the summer months, but these weaken in colder months. DO and pH at this site also exhibit tidal-cycle patterns at times, particularly in fall and late summer, with lower pH and DO occurring at low tides. At the Lower Duplin (LD) site, there is again a seasonally varying diel signal for temperature but little or no diel pattern for pH or DO. All three of these variables at LD show some patterns versus the tide, with higher temperatures and lower pH and DO values recorded at LD low tide. Salinity has a strong and fairly regular M₂-dominant cycle at the LD site, with higher amplitudes in January–April. In contrast, salinity at the HD site displays trends of 5–10 ppt lasting a fortnight or more, with complex and inconsistent diel- and tidal-cycle patterns, which we believe to be influenced by freshwater intrusion events that created some inconsistency in the cyclic fluctuations found. Mild hypoxia, with DO at or slightly below 20% saturation, occurred at both sites with some regularity in late summer, usually associated with the pattern of declining DO at low tide.

The lagoons that border the east coast of the Florida peninsula provide an opportunity to study water chemistry and phytoplankton characteristics over a wide range of water residence and nutrient load conditions. This article includes the results of a 2-year study of eight study sites. The northern half of the sampling range included four sampling sites within the newly established Guana Tolomato Matanzas National Estuarine Research Reserve. The southern half of the sampling range consisted of four study sites distributed in ecologically distinct sub-basins of the Indian River Lagoon. The Guana Tolomato Matanzas National Estuarine Research Reserve and Indian River Lagoon include estuaries with water residence times ranging from days to months and watersheds with widely differing nutrient load characteristics. The results of this study revealed wide temporal and spatial variability of physical and chemical characteristics. Mean salinities for the study period ranged from 9.7 to 31.5‰ over the eight sites. Mean orthophosphate and total phosphorus concentrations ranged from 0.26 to 1.55 μM and 1.45 to 3.00 μM, respectively. Mean dissolved inorganic nitrogen and total nitrogen concentrations ranged from 3.14 to 9.77 μM and 26.43 to 71.14 μM, respectively. Individual phytoplankton standing crops, in terms of chlorophyll a concentrations, ranged from less than 1 μg L⁻¹ to more than 60 μg L⁻¹. Comparisons of the relationships between nutrient and phytoplankton standing crops at the eight study sites indicated that water residence times and nutrient loads provided important insights into the basis for observed temporal and spatial patterns of variability. Indices for water residence time and nutrient load were determined for each site. A combination of the character of watershed inputs and residence time was most useful in interpreting patterns of nutrient concentrations, whereas water residence time appeared to be the pre-eminent factor dictating phytoplankton standing crop potential among the eight study sites.

We describe the use of Monie Bay as a natural experiment to evaluate the effect of system-level nutrient enrichment on natural bacterioplankton communities. Monie Bay, a component of the Chesapeake Bay National Estuarine Research Reserve System, is a subestuary of the Chesapeake Bay, consisting of a shallow semienclosed bay and three tidally influenced creeks varying in their agricultural land use and freshwater inputs. As part of a 2-year study in this system, we identified distinct spatial and seasonal patterns in ambient nutrient concentrations, salinity, and source and quantity of organic matter that were related to differences in agricultural practices and watershed characteristics among the three tidal creeks. Principal components analysis identified freshwater delivery of nutrients and temperature as key factors driving the overall variability of this system. Despite significant variability in nutrient concentrations and bacterioplankton production (BP) throughout the year, we observed persistent response of bacterioplankton to nutrient enrichment, as evidenced by a comparison of 2-year averages in agriculturally developed Little Monie Creek (LMC) relative to the undeveloped Little Creek (LC), and by a comparison of the nutrient-enriched upper estuary of LMC to sites nearer the open bay. Bacterioplankton responded positively to pulsed nutrient availability, with elevated rates of BP associated with agriculturally derived nutrient inputs to the Monie Bay system. Freshwater inputs play an important role in mediating the response of bacterioplankton to nutrient enrichment, as evidenced by relatively low estimates of BP in the freshwater-dominated, agriculturally developed Monie Creek. This response is attributed to changes in organic matter quality in the system and the direct effect of salinity on bacterioplankton community metabolism.

Salt marshes provide a buffer between the terrestrial landscape and estuaries and may be important in preventing the movement of land-derived nutrients into coastal waters. We examined the response of S. patens in the field to additions of dissolved inorganic nitrogen (N) and phosphorus (P) and found significant (p < 0.05) positive N effects on aboveground biomass, leaf chlorophyll, tissue nutrient concentrations, and induction of fluorescence kinetics of chlorophyll a. Mean endomycorrhizal colonization among treatments was 22%, and fungal colonization ranged from 2% to 61% in the plots. We found no significant effect of N or P on endomycorrhizal colonization, but there was a significant inverse relationship (r = −0.66, p = 0.005) between the belowground biomass and fungal colonization. This study showed that S. patens could sequester 44–100% of the added N and 82–100% of the added P in its leaves, roots, and rhizomes. However, it is unclear how long-term nutrient overenrichment and the resulting changes in the S. patens–microbe–sediment system might alter the marsh buffering capacity.

Submerged aquatic vegetation (SAV) is widely recognized as an important habitat and indicator of water quality in large rivers and estuaries. Despite the perceived importance, system-wide assessments of cover, susceptibility to change, and ecological functioning are rare because of the geographical scope and multi-disciplinary expertise required. A collaboration between scientists, estuarine managers, and environmental educators was initiated to map the SAV and the Eurasian water chestnut (Trapa natans) in the Hudson River estuary from Hastings-on-Hudson north to Troy, New York. These groups provided diverse scientific and estuarine management expertise to enable the first broad delimitation of SAV in the Hudson and sampling of beds to describe abundance, biomass, and species composition and to address management and education needs and opportunities. The areal extent of SAV based on a combination of 1995 and 1997 photographs in the study area was 1,802 hectares (4,453 acres), ∼6% of the river area and ∼18% of the shallows (defined as less than 3 meters deep at low tide). Trapa natans covered 575 hectares (1,421 acres), 2% of the river area and 6% of the shallows. In the most heavily vegetated portion of the Hudson (approximately 150–200 kilometers of river), the coverage by plants (both SAV and T. natans) approached 25% of the river bottom area. Results of this work have been integrated into the federal and state regulatory processes, local resource users, and local science education programs. Finally, we have initiated a volunteer SAV monitoring program.

The influence of seagrasses on water quality was investigated seasonally from permanent stations located along transects across vegetated and formerly vegetated sites in shoal regions of the Chesapeake Bay National Estuarine Research Reserve in Virginia. The effect of the seagrass bed on conditions inside compared to outside the bed varied seasonally and could be related to bed biomass and development. During spring (April to June), the rapidly growing seagrass bed was a sink for nutrients, suspended inorganic particles, and phytoplankton, whereas during the summer, as bed dieback progressed, resuspension and release of nutrients were observed. Reductions in suspended particle concentrations and light attenuation were generally not measurable until bed biomass exceeded 50–100 gdm/m² or 25–50% vegetative cover. During April, when nitrate levels in adjacent channel waters were observed to be highest (>10 μM), rapid uptake, equivalent to 48% of nitrogen requirements for seagrass growth, reduced inorganic nitrogen standing stocks by 73% within the bed compared to outside of it. An unvegetated site that previously supported seagrass demonstrated little capacity to reduce measurable levels of suspended particles or nutrients, and resuspension of bottom sediments contributed to higher levels of suspended particle concentrations and turbidity in the unvegetated shallows compared to adjacent waters. The capacity of seagrass beds to improve local water-quality conditions, such as turbidity and nutrients, during the spring when suspended particle concentrations are highest may be key to their continued long-term survival in this lower bay region. High levels of spring turbidity, which have been related to seagrass declines in this area, can be mediated by dense seagrass structure, but largely unvegetated areas are unlikely to modify conditions to permit survival of first-year recruits or transplants through the summer. Therefore, water-quality conditions that are suitable for recovery are likely greater than those required for continued survival of existing seagrass beds. Given this, statistically derived estimates of water-quality conditions or habitat requirements that are usually obtained from measurements in areas adjacent to existing seagrass beds should be used with caution. Although suitable for predicting the maintenance of existing beds with adequate biomass and structure, they may underestimate the levels needed for restoration and recovery of many currently unvegetated sites.

Understanding the circulation and exchange rates of water masses in an estuary is critical to understanding the movement and recruitment patterns of planktonic propagules and how these patterns relate to the distribution and abundance of adults. Forests of bull kelp (Nereocystis luetkeana) are complex three-dimensional habitats that can support tightly linked trophic interactions between primary producers, herbivores, and carnivores. Therefore, the spatial distribution of this important habitat can affect local food webs. Kelp forests in Kachemak Bay, Alaska, were mapped from 2000 to 2002 using low-altitude aerial photography. Over the 3 years, kelp forests were found only in the outer basin, and only a few attached sporophytes were found in the turbid and lower-salinity inner basin. Many biotic and abiotic factors can affect the dispersal and development of kelp. We tested the hypothesis that decreased salinity and light intensity in the inner basin limit the spatial distribution of Nereocystis sporophytes in this system. Transplant experiments were conducted between the marine and estuarine endpoints of kelp forest distribution. These experiments suggest that the growth of Nereocystis sporophytes transplanted from the marine to the estuarine endpoint was impeded, but that they could survive under estuarine conditions. We tested a second hypothesis, that estuarine circulation patterns control Nereocystis sporophyte distribution. Hydrographic measurements and circulation studies suggest that a strong baroclinic jet develops in the late summer and fall and may prevent Nereocystis spore dispersal into the inner basin. The cyclonic surface circulation in the outer basin may contribute to the observed spatial distribution of kelp forests in this system.

The timing and quantity of fresh water flowing into the Rookery Bay National Estuarine Research Reserve, southwest Florida, have been altered by channelization of natural watershed sheetflow and increases in freshwater storage for aquifer recharge and irrigation. As part of the ongoing Everglades Restoration Initiative, the Southern Golden Gate Estates (SGGE) Restoration and Henderson Creek Freshwater Inflow Restoration Projects are opportunities to re-establish watershed sheetflow and restore the natural timing and quantity of fresh water flowing into the Reserve's estuaries. For 3 years, data loggers have been used to record water quality at continuous half-hour intervals, and Hester-Dendy artificial substrates have been used to sample oyster reef crab populations each month in four estuaries managed by the Reserve. These four estuaries differ in their seasonal and annual salinity patterns because of varying degrees of anthropogenically altered freshwater inflow. Our observations indicate that the relative abundances of the euryhaline (Eurypanopeus depressus) and stenohaline (Petrolisthes armatus) crab populations provide a useful biological performance measure to guide freshwater inflow restoration projects. This manuscript examines this metric as applied to the SGGE and Henderson Creek Freshwater Inflow Restoration Projects.

The benthic macrofaunal community of the Mullica River–Great Bay estuary in the Jacques Cousteau National Estuarine Research Reserve is characterized by both small-scale and large-scale distribution patterns that can be correlated to gradients in physicochemical parameters. Sediment composition is a major factor regulating the local distribution of benthic assemblages in the estuary, with the amount of silt-clay being particularly important. For example, one suite of benthic fauna (i.e., Ampelisca verrilli, Ensis directus, Haustorius arenarius, Pygospio elegans, and Oxyurostylis smithi) reported in the estuary has been found only in sediments with less than 20% silt-clay, whereas another (i.e., Acteocina canaliculata, Lumbrineris tenuis, Maldinopsis elongata, Tellina agilis, Turbonilla sp., and Unciola irrorata) has been observed only in sediments with more than 38% silt-clay. Other physicochemical factors (e.g., organic carbon content of the sediments, dissolved oxygen levels, bottom currents, and turbidity) might also influence the local distribution patterns of the fauna. On the estuary scale, environmental gradients from upriver to down-bay regions strongly affect the distribution of the benthos over broader spatial areas. Hence, four distinct regional assemblages of benthic invertebrates have been identified in the Mullica River–Great Bay estuary, including river-, bay-, lower bay–, and estuary-wide forms. The dominant assemblage—the estuary-wide forms distributed along the length of the estuary—consists of the most abundant populations with the widest salinity tolerances. Examples are Ampelisca abdita, Corophium cylindricum, Cyathura polita, Notomastus latericeus, Polydora ligni, Scoloplos robustus, and Turbonilla sp. Because Great Bay exhibits marked changes in sediment type from predominantly sands in the eastern perimeter to generally finer deposits along the western margin, the abundance, species richness, and species composition of benthic invertebrates vary considerably over relatively small spatial scales.

Side-scan sonar imaging conducted in Great Bay, New Jersey, during August 2003 reveals local variations in acoustic backscatter from the seabed that can be related to small-, medium-, and large-scale bedforms. Analysis of 600-kilohertz side-scan sonar data collected at a System-Wide Monitoring Program (SWMP) survey site of the Jacques Cousteau National Estuarine Research Reserve shows a relationship between backscatter intensity, bathymetry, and changing seabed morphology. Side-scan sonar records obtained at the survey site in Great Bay via deployment of an autonomous underwater vehicle (Remote Environmental Monitoring UnitS) provide in-depth characterization of an array of complex and multiscaled bedforms and associated benthic habitats. Bedforms documented within the swath map region by side-scan sonar imaging include constructive transverse forms, notably ripples, dunes, and sand waves. These bedforms are valuable for assessing potentially important habitats for benthic invertebrate and demersal finfish populations.