The National Estuarine Research Reserve System (NERRS) consists of an integrated network of 27 reserve sites in 19 biogeographical subregions. These estuarine reserves are protected sites where comprehensive databases are compiled to characterize the natural and anthropogenic processes governing ecosystem stability and change. Data collected by research and monitoring programs of the NERRS provide the foundation for sound coastal management decision-making. Three principal areas of research and monitoring are targeted by the NERRS: (1) abiotic factors, including meteorological, water quality, and physical conditions; (2) biotic features, including both flora and fauna; and (3) land use and habitat change characterizations. Baseline conditions and trends in physical, chemical, and biological parameters are vital for evaluating changes that occur in response to various environmental stressors and long-term climate change throughout the network of estuarine ecosystems. The NERRS is a particularly effective program because its research and monitoring activities occur in all geographical regions of the United States and almost every recognized climatic zone. Because of the geographic expanse of the NERRS and its intensive and extensive research and monitoring initiatives, an ideal platform exists to characterize both the short-term variability and long-term changes in estuarine systems nationwide and to make these results available to support informed decision-making and increased public awareness of coastal systems.

Circulation and flushing inside the lagoon system of Guana Tolomato Matanzas National Estuarine Research Reserve (GTMNERR or GTM) have been studied using a three-dimensional numerical circulation model CH3D. The lagoon system includes two tidal inlets (St. Augustine Inlet and Matanzas Inlet). To ensure accuracy in model results, we extend the model domain to include a large portion of the coastal water and the Ponce de Leon Inlet in the south. Water levels on the open boundaries are provided by the East Coast (2001) ADCIRC Tidal Database. Model simulations of barotropic and baroclinic circulation from April 1 to May 31, 2004, produced reasonable water levels at numerous stations inside the GTM. Simulated salinity results are not as good because of the lack of freshwater inflow data inside the GTM and salinity data offshore. Using the simulated flow fields, we solve the three-dimensional transport equations for conservative species, and determine the flushing characteristics inside the GTM in terms of the 50% renewal time of the conservative species within each of eight segments, which are selected by considering the geographical features and proximity to tidal inlets and rivers. The flushing results indicate that tide is the most dominant flushing mechanism, while river and salinity are important flushing mechanisms for segments that are far from the tidal inlets. The normalized flushing times, defined as the 50% renewal time divided by the volume of the segment, are calculated for the eight segments and compared with each other. Comparing the “normalized” flushing time at all segments, a relative flushing ranking (RFR) is generated that ranks the “normalized” flushing time from the shortest to the longest as follows: segment 2 (includes St. Sebastian), segment 8 (near Ponce Inlet), segment 3 (includes Fort Matanzas), segment 7 (near Ponce Inlet), segment 1 (includes Pine Island), segment 4 (includes Pellicer Creek), segment 6 (includes High Bridge Road), and segment 5 (includes Bings Landing). This quantitative ranking of flushing characteristics inside the GTM is made possible because of the use of a three-dimensional numerical circulation and transport model that incorporates the effect of hydrodynamics on flushing. These results provide much more quantitative information than the simple empirical residence time indices (1–4) developed for the GTM in a previous study. CH3D was also applied to simulate the circulation during January 25 to February 3, 2006. Simulated currents inside the St. Augustine Inlet on February 2, 2006, compare favorably with the currents measured by Acoustic Doppler Current Profiler (ADCP). Model simulated flow rates through St. Augustine and Matanzas inlets reproduced measured data on July 1 and June 16, 2004, respectively. Model-simulated currents and water levels improved when the flooding-and-drying version of the model was used. The three-dimensional modeling approach can be used to provide sguidance on resource management and the development of sampling strategies for several ongoing and prospective biogeochemical studies in the GTM.

The objective of this study was to document the effects of extreme wind and rainfall conditions associated with tropical storms on physiochemical variability in a tidal creek, Pellicer Creek, in northeast Florida. High-frequency salinity and meteorological data from the Guana Tolomato Matanzas National Estuarine Research Reserve were examined at a range of temporal scales, from 30-minute to annual intervals. Monthly measures of nutrient and water clarity parameters were compared to salinity variations. It was hypothesized that the four tropical storms impacting the region in 2004 (i.e., Charley, Frances, Ivan, and Jeanne) altered tidal regimes and watershed inputs to Pellicer Creek sufficiently to generate water column conditions that deviated significantly from nonstorm periods. The four tropical systems of 2004 suppressed tidally induced salinity variations. Strong northeasterly winds associated with the storm events initially prompted salinity spikes. However, high rainfall levels during the course of each event ultimately caused strong declines in salinity for extended periods of time. Nitrogen concentrations in Pellicer Creek were significantly elevated after storm events. Because primary production in many of the coastal environments along the east coast of Florida, as well as around the world, is nitrogen limited, increases in nitrogen input represent a potential for enhanced algal production and biomass. Given the major changes in watershed characteristics and global climate patterns expected in future years, the ability to predict the influences of these changes on the estuarine environment will be an essential part of designing, implementing, and justifying management efforts.

Since 1985, various long-term monitoring programs have been in place in the Apalachicola Bay area that can be utilized to determine the effects of tropical storms and hurricanes on the natural resources of the area. The size, speed of movement, severity, angle and direction of landfall, as well as storm surge height and the amount and location of precipitation all play a role in determining impacts. Short-term impacts seen in the bay from these tropical events include water quality alterations, such as salinity and turbidity changes, water level changes, and loss of sea turtle nests. Long-term impacts include changes to the structure of the beach, dunes, and bayside areas on a barrier island, loss of or changes in submerged aquatic vegetation distribution, and the physical alteration of oyster reefs as well as oyster populations. In particular, Hurricane Dennis in 2005 caused the complete loss of fresh and brackish submerged aquatic vegetation in the upper areas of the bay. Larger storms in 1995 and 2004, such as Hurricane Opal and Hurricane Ivan, caused relatively little damage to natural resources. Hurricane Elena in 1985 caused massive damage to the local oyster industry, which took several years to recover.

Because hypoxia can have catastrophic effects on estuarine ecosystem health, a critical coastal resource management need is the ability to quantify and compare the relative severity of hypoxic events in terms of their potential for ecological impact. This study makes use of continuous, high-frequency water quality monitoring data available through the National Estuarine Research Reserve's System-Wide Monitoring Program to explore a quantitative index approach that captures the transient nature of hypoxic events and allows for their comparison across space and time. The conceptual model explores various time and concentration thresholds for defining “events,” which then allows for ranking their severity in terms of duration and concentration. In our example, we have borrowed from the familiar hurricane categorization index to create an analogous hypoxic event severity index (1–5), with higher values indicating more ecologically damaging events. We demonstrate that the model provides a convenient way to quantify and compare the frequency and severity of hypoxia over 4 years at one site and between two widely separated locations over 3 years.

The National Estuarine Research Reserve System represents a diverse collection of ecosystems among which environmental conditions differ dramatically, making it inherently difficult to determine the extent to which patterns and properties identified in one estuary are transferable to those of any other. The primary objective of our study was to develop a multivariate classification framework for comparison of these estuaries and identify the primary sources of environmental variability in each. Using a 4-year dataset from the National Estuarine Research Reserve System-Wide Monitoring Program, combined with principal components analysis, we identified distinct patterns among 21 reserves that allowed grouping based on the primary factors shaping physicochemical variability. Salinity and temperature were the primary factors shaping variability in the reserves, an observation that was corroborated by similar multivariate analysis of data from 33 published studies of non–National Estuarine Research Reserve systems representing a wide range of coastal and estuarine waters. We then investigated the effect of temperature and salinity on biological processes in these systems by using the ratio of bacterial production to chlorophyll-a as a response variable. Salinity and temperature had different but significant effects on bacterial production/chlorophyll-a ratios, suggesting in turn that these properties contribute to the balance between autotrophic and heterotrophic planktonic processes in estuarine ecosystems. Our study confirms the universal role of salinity and temperature in shaping the variability among even the most diverse systems and provides a valuable classification framework for comparison of reserves within the context of the entire National Estuarine Research Reserve System. Use of this classification approach may provide insight into the extent to which results from investigative studies in one reserve may be applicable to others, a valuable application when the effect of environmental stressors is considered.

Nutrient temporal and spatial distributions were evaluated, in addition to budgets and fluxes derived from the Land-Ocean Interaction in the Coastal Zone (LOICZ) biogeochemical model, to determine dissolved organic matter and inorganic nutrient distribution, flux, and fate in the Mullica River–Great Bay Estuary. Seasonal cycles were observed for dissolved organic carbon (DOC), nitrogen (DON), and phosphorus (DOP) with increasing concentrations from spring to fall and maximum concentrations in summer/early fall. Annually, the estuarine system was a net source of DOC ( 5 mol m⁻² y⁻¹), DON ( 0.08 mol m⁻² y⁻¹), and dissolved inorganic phosphorus (DIP, 0.010 mol m⁻² y⁻¹), a net sink of dissolved inorganic nitrogen (DIN, −0.28 mol m⁻² y⁻¹), and in approximate balance of DOP (0.001 mol m⁻² y⁻¹). Overall, the upper estuary and mid-estuary served as net sinks for most nutrients, whereas the lower estuary served as a net source. Annual mean nutrient export from the lower estuary to the nearshore coastal region was 3 mol m⁻² y⁻¹ for DOC, 0.08 mol m⁻² y⁻¹ for DON and DIN, 0.006 mol m⁻² y⁻¹ for DOP, and 0.017 mol m⁻² y⁻¹ for DIP. In comparison, annual mean watershed DIN input (0.02 mol m⁻² y⁻¹) was approximately two times greater than DON input (0.01 mol m⁻² y⁻¹), whereas watershed DOP input (0.24 mmol m⁻² y⁻¹) was approximately two times greater than DIP input (0.10 mmol m⁻² y⁻¹). The lower estuary may serve as a potentially significant source of nutrients for primary production in the nearshore coastal region. Differences in nitrogen and phosphorus pools between watershed inputs and lower estuary exports suggest that the Mullica River–Great Bay estuarine system serves an important role in the cycling of dissolved nitrogen and phosphorus, ultimately controlling the fraction of organic and inorganic nitrogen and phosphorus delivered to the coastal zone.

Long-term trends and relationships between large mesozooplankton (1.5–20 mm) and the physical environment were used to investigate impacts of climate change and variability in the North Inlet estuary, South Carolina. Biweekly collections (365 μm) from 1981 to 2003 demonstrated distinct seasonal patterns and large interannual fluctuations in abundances. Significant long-term decreases in abundances were observed for total zooplankton and 12 taxa (e.g., Gobiosoma larvae, chaetognaths, and adult shrimps), whereas 14 others, including some of the most abundant constituents, did not change (e.g., mysids, amphipods, crab megalopae, and Palaemonetes larvae). The composition of the fauna was similar at the beginning and end of the 23-year period. A significant long-term increase in winter water temperature (2.6°C) and a decrease in summer salinity (3.2) were determined. Relationships between physical conditions and taxa varied in strength and direction, and most did not agree with their long-term trends. However, some major taxa appeared to respond to climate variability, including the timing and intensity of El Niño or La Niñ a events. Although changes in the North Inlet mesozooplankton were minor compared to fauna in northern waters in recent decades, a trend toward the freshening and warming of this system could alter processes including larval recruitment, secondary production, and trophic interactions. The design of long-term sampling programs must consider effects of tide and time of day on zooplankton. The National Estuarine Research Reserve System provides an ideal platform for the collection of time series measurements that are critical to the understanding of climate change on biological communities.

Numerous studies have documented the invasion of wetland plants, yet few have tracked the invasion process from its early stages to subsequent large-scale, plant-community changes. The invasion of Phragmites australis (common reed) into the Great Lakes region is a recent phenomenon, facilitated by a decline in water lake levels. The spread of P. australis was tracked in the Old Woman Creek National Estuarine Research Reserve, a 60-ha Lake Erie coastal wetland, using a combination of low-altitude aerial photography and ground surveys during the period from 1993 to 2005. Since the late 1990s, the Old Woman Creek wetland has shifted from a predominantly open-water system to a shallow, water-emergent system. This shift has coincided with a decline in Lake Erie water levels, which are now closer to the long-term mean water level. Aerial photographs for the period 1993–2005 show a transition from the floating leaf Nelumbo lutea (American lotus), to a mixed-emergent community, to increasingly large monotypic beds of P. australis. This wetland perennial grass currently occupies about 22% of the lower wetland and is also a significant component of the emergent community that covers approximately 30% of the lower wetland. The emergent community and P. australis comprised less than 1% of the wetland area in 1993.

Salt marshes, eelgrass beds (Zostera marina), and benthic macroalgae frequently occur in close proximity along the steep tidal channels of Pacific Northwest estuaries, where they constitute distinct patches of transitional land-margin habitat. The eelgrass beds and adjacent salt marshes within the South Slough National Estuarine Research Reserve, Oregon, provide an opportunity to investigate commonalities and differences between two ecological-indicator communities that are often separated by only a few meters. The principal objectives of this study are to establish a series of adjacent eelgrass and salt marsh assessment and monitoring sites within different hydrographic regions of the South Slough estuary and to characterize initial temporal and spatial changes in the composition of the plant communities in accordance with new field protocols developed by the National Estuarine Research Reserve System (NERRS) and by SeagrassNet. Eelgrass beds and emergent salt marsh communities were sampled at three study sites located along the estuarine gradient of the South Slough (43°20′N, 124°19′W). Study sites were established at (1) Collver Point (marine-dominated region), (2) Valino Island (polyhaline region), and (3) Danger Point (riverine/mesohaline region). Ambient water parameters and water column nutrients were monitored throughout the study period (2004–05) as part of the South Slough NERR System-Wide Monitoring Program. Periodic assessment of Rod Sediment Elevation Table (RSET) stations established within the eelgrass beds revealed that surface elevation increased at a rate of about 0.84 mm mo⁻¹ at the Valino Island site but decreased at a rate of about 0.44 mm mo⁻¹ at the Danger Point study site. Metrics of community richness, diversity, and species equitability indicate that the adjacent salt marshes and eelgrass beds develop community characteristics within the South Slough that are strongly reflective of their location along the estuarine gradient. The community composition, spatial cover, and density of macrophytes within the salt marsh and eelgrass communities were very similar between the Collver Point and Valino Island study sites, where mean monthly salinities in the tidal channel ranged between 25 and 32, and water temperatures were moderate (10–16 °C) throughout the year. In contrast, the salt marsh communities and eelgrass beds were distinctly different at the Danger Point study site, where mean monthly salinities ranged between 10 and 20, and water temperatures were much warmer in summer (20 °C) than in winter (9 °C). These intertidal salt marshes and eelgrass beds are highly productive and ecologically important components of the South Slough estuarine ecosystem despite their low richness of macrophyte species and relatively low metrics of community diversity. Recognition of these landscape-level differences in composition and productivity of submersed and emergent vegetation is important in the South Slough because the plant communities have potential to serve as reference sites to gauge the effectiveness of off-site habitat restoration and enhancement efforts.

We investigated the effects of several environmental factors on eelgrass abundance before, during, and after widespread eelgrass diebacks during the unusually hot summer of 2005 in the Chesapeake Bay National Estuarine Research Reserve in Virginia. Systematic sampling with fixed transects was used to investigate changes in eelgrass abundance at downriver and upriver regions of the York River Estuary. Concurrently, continuous and discreet measurements of water quality were made at fixed stations in each area within the eelgrass beds from 2004 through 2006. Results indicate nearly complete eelgrass vegetative dieback during the July–August period of 2005, in contrast to the more seasonal and typical declines in the summer of 2004. Losses were greatest in the deeper areas of the beds and at the upriver site where light availabilities were lowest. Recovery of eelgrass during 2006 was greater in the downriver area, especially at mid-bed depths. By the fall of 2006, no shoot vegetation remained at the upriver site. In 2005, the frequency and duration of water temperatures exceeding 30°C were significantly greater than that of 2004 and 2006. Additionally, the frequencies of low dissolved oxygen excursions of 1–3 mg L⁻¹ during this period were greater in 2005 than 2004 or 2006. These results suggest that eelgrass populations in this estuary are growing near their physiological tolerances. Therefore, the combined effects of short-term exposures to very high summer temperatures, compounded by reduced oxygen and light conditions, may lead to long-term declines of this species from this system.

A detailed submerged aquatic vegetation (SAV) study was conducted in Little Egg Harbor (39°35′N, 74°14′W), New Jersey, a lagoonal estuary located within the boundaries of the Jacques Cousteau National Estuarine Reserve, to assess the demographic characteristics and spatial habitat changes of Zostera marina beds over an annual growing period and to determine the species composition, relative abundance, and potential impacts of benthic macroalgae on seagrass habitat in the system. Two disjunct seagrass beds in Little Egg Harbor, covering an area of ∼1700 ha, were sampled at 10 equally spaced points along six, east–west-trending transects in spring, summer, and fall (June–November) of 2004. During this period, 180 seagrass samples were collected at 60 transect sites, together with an array of water quality measurements. Results of this investigation indicate that both aboveground and belowground biomass of seagrass peaked during June–July and declined significantly into the fall months. Mean aboveground biomass ranged from 18.22 to 106.05 g dry wt m⁻², and mean belowground biomass from 50.48 to 107.64 g dry wt m⁻². Biomass values were higher along the northernmost sampling transects than along those farther to the south. They were also higher at interior sampling sites within the seagrass beds than along the bed margins for two of the three sampling periods. Mean seagrass blade length was consistent throughout the study period, averaging 31.83–34.02 cm. The percentage of cover by seagrass, which ranged from 21% to 45%, peaked in June–July at the time of maximum seagrass biomass. The percentage of cover by macroalgae was lower than that of seagrass, averaging 13%–21%, with maximum cover occurring in August–September. Most of the macroalgal species collected in the seagrass beds were red algae, although the dominant species was typically the green seaweed, Ulva lactuca. During the 6-month study period, no brown tide (Aureococcus anophagefferens) blooms were recorded, and phytoplankton abundance did not appear to cause shading problems for seagrass in the system. However, benthic macroalgal blooms were observed in the seagrass beds, most notably U. lactuca. These blooms blanketed parts of the seagrass beds and appeared to degrade them over extensive areas. Nutrient enrichment, elevated turbidity levels, and prop scarring are anthropogenic factors that may significantly influence seagrass beds in Little Egg Harbor during the growing season.

A benthic habitat assessment study conducted in the Barnegat Bay-Little Egg Harbor Estuary from June to November 2006 reveals that boat-based videographic imaging is comparable to in situ diver observations for determining the occurrence and percent cover of seagrasses in actively growing beds. A Seaviewer Sea Drop camera and recorder unit deployed along 12 transects in the estuary generated 331 images of seagrass habitat during the study period. A comparison of video still images with data derived from diver observations indicates consistent results in terms of the presence/absence and percent cover of seagrass on the estuarine floor throughout the seagrass growing season. Plots of the percent cover of seagrass recorded by the camera system vs. in situ diver observations reveal a high correlation for the June–July, August–September, and October–November sampling periods (R² = 0.936, 0823, and 0.894, respectively) as well as for the entire June–November sampling period (R² = 0.888). A kappa statistic calculated for the presence/absence of seagrass in the estuary (0.83) reflects a nearly perfect level of agreement between the two methods (camera and diver) of data collection. In addition to generating rapid databases, digital underwater video imaging requires less field time than the use of divers and other traditional field monitoring methods. Digital videographic files can also be post-processed, geolocated using a global positioning system, analyzed by multiple investigators, and stored for later analysis, thereby offering several other advantages over traditional in situ monitoring techniques in shallow estuarine systems.

Tidal exchange was restored to the flow-restricted, 2.3-ha Potter Pond salt marsh on Prudence Island in the Narragansett Bay National Estuarine Research Reserve in April 2003. Ecological monitoring was conducted for 1 year before and 2 years after restoration to quantify ecological changes. Simultaneous monitoring was conducted in a nearby marsh that served as an experimental control. Tidal restoration increased the tide range in Potter Pond from approximately 4 cm in 2000 to 120 cm in 2003. After 2 years of restoration, the height of Spartina alterniflora remained unchanged, and the same was true of the composition of the emergent marsh vegetation community. However, by 2004, the percent cover of live Phragmites australis decreased by 69%, and the average height of Phragmites decreased by 76 cm. Seven additional bird species were observed at Potter Pond after 1 year of restoration, and the number of birds observed increased from 6 to 85 per viewing effort, mostly due to large numbers of shorebirds using the newly exposed mud flats. Nekton density decreased from 100 m⁻² to 38 m⁻² after 1 year, probably because of the change from subtidal to mostly intertidal conditions and increased predation by birds. Initial results from monitoring demonstrate that restoration of the Potter Pond marsh complex improved tidal exchange, negatively impacted Phragmites, and increased bird use, resulting in an overall shift to a more natural functioning salt marsh system. This study also demonstrates that restoring even very small tide-restricted marshes can result in impressive ecological improvements.

Long-term trawl samples for white shrimp, Litopenaeus setiferus, collected within the Ashepoo, Combahee, Edisto Basin National Estuarine Research Reserve and adjacent waters were analyzed for trends in relative abundance and life history patterns. Milder winters are thought to have contributed to high population levels of white shrimp here, as seen along the rest of the southeastern coast of the United States. In addition to winter water temperature, regression analysis indicated a significant increase in salinity over time in the reserve and a significant relationship between percent saturation of dissolved oxygen and shrimp abundance in the summer. Relatively larger shrimp were collected in the spring and at open water locations in St. Helena Sound, reflective of normal growth and migration. Such baseline data should prove valuable for assessing future sustainability of shrimp stocks, especially if recent climatic trends of drought occur in the future.

The spatial and temporal distributions of decapod crustacean and juvenile fish species in the Ashepoo, Combahee, and South Edisto (ACE) rivers in the ACE Basin National Estuarine Research Reserve were examined from 1993 to 1999. Nekton samples were collected monthly during slack low to early flood tide by bottom trawl from 12 fixed stations (four stations/river) along the salinity gradient in the reserve. During the 6-year survey, 79 species of fish and 26 decapod crustacean species were caught. Coastal marine species represented more than 80% of the species collected during the survey; the remaining finfish were permanent residents, freshwater, and diadromous species. Star drum (Stellifer lanceolatus), Atlantic croaker (Micropogonias undulatus), bay anchovy (Anchoa mitchilli), and spot (Leiostomus xanthurus) constituted >68% of the total number of individual fishes collected. White shrimp (Litopenaeus setiferus) and brown shrimp (Farfantepenaeus aztecus) constituted ∼87% of the total number of individual decapods collected. Fish and decapod crustacean assemblage structure in the three rivers were analyzed for spatial and seasonal patterns. Spatial distribution of the species assemblages in the estuarine systems appeared to be strongly influenced by the physiological tolerances of the individuals to salinity gradients in the study area. Seasonal variations in species diversity and abundance appeared to be related to migration and recruitment of species to the estuarine system, and there were two annual recruitment cycles: winter–spring (October to March) and summer–fall (April to September). The variations in species diversity among the stations in the mesohaline zone were driven by the abundance of the dominant species.

The spread of invasive exotic vegetation is a serious threat to native habitats in South Florida. The exotic Australian pine proliferates in coastal areas forming monocultures. They fall over easily during strong winds, making nesting habitat inaccessible to sea turtles. The objective of this study was to determine if removing the standing pines would alter hatchling sex ratios of sea turtles because nest temperatures could increase in the absence of shade provided by the exotic pine species. A total of 274 Hobo temperature data loggers were deployed in sea turtle nests on Keewaydin Island, Collier County, Florida, during the 2001, 2002, 2004, 2005, and 2006 nesting seasons to monitor the effect of Australian pine removal on incubation temperatures. The results indicated that shading from the pines did not affect incubation temperatures differently than native vegetation. Therefore, removing the pines did not alter hatchling sex ratios. During the study, southwest Florida was affected by several storm events and hurricanes washing out 57 data loggers and causing an additional 15 data loggers to malfunction. Nest temperatures during the thermosensitive period ranged from 23.24°C to 34.85°C with mean temperatures ranging from 26.61°C to 31.51°C. Hatchling sex ratios were predicted based on mean incubation temperatures during the thermosensitive period. The predictions indicated that nests on Keewaydin Island were producing predominately mixed ratio and male-biased clutches. Dead hatchlings were collected for histological examination to substantiate sex ratio predictions. Histology samples were female-biased in 2002 and male-biased in 2001 and 2004.

In 1986 and 1987, the New York State Department of Environmental Conservation and the Hudson River Foundation sponsored a study of avian breeding habitats in six tidal marshes on the Hudson River Estuary. Local concern prompted a repeat of this study at Iona Island Marsh in 2004 and at four of the marshes in 2005 (Iona Island Marsh, Constitution Marsh, Tivoli North Bay, and Stockport Flats). This study had three main objectives: (1) to document bird species breeding in these four marshes, (2) to determine how the marsh-breeding populations have changed since the 1986–87 study, and (3) to relate the spatial distribution of marsh-nesting species to measurable habitat variables within marshes. A total of 3522 observations of birds, representing 83 species, were recorded from April 28, 2005, to June 30, 2005. These observations were made by sampling 109 fixed observation stations five times using both visual and vocalization sampling methods. Nineteen of those species are dependent on emergent marsh habitats. The most common marsh-dependent species encountered during this study were Red-winged Blackbird (Agelaius phoeniceus) and Marsh Wren (Cistothorus palustris). These two species each accounted for 23–47% of the marsh-dependent guild at Constitution Marsh, Tivoli North Bay, and Stockport Marsh. Marsh Wrens were nearly absent from Iona Island Marsh (<1.0%); there, Red-winged Blackbirds accounted for more than 77% of the marsh bird community. Red-winged Blackbirds also dominated the marsh avian communities at Constitution and Stockport Marshes. Bird species diversity decreased significantly since 1986–87 at Iona Island and Constitution Marshes. Decreased diversity corresponds with an increase in the density of Red-winged Blackbirds. At Iona Island Marsh, this shift in the avian community to almost entirely Red-winged Blackbirds coincided with a shift of the plant community dominance from narrowleaf cattail (Typha angustifolia) in 1986–87 to common reed (Phragmites australis) in 2004–05. This shift was not evident at Constitution Marsh, Tivoli North Bay, or Stockport Marsh, although the number of Phragmites australis has also expanded at these sites. In addition to our survey, we found a total of 230 nests in 2005. Major findings of the bird nest searches were (1) the very low density of nests found at Iona Island Marsh (five nests total in 2004 and 2005), (2) the most common nest encountered at the other three marshes was that of the Marsh Wren (83% of total nests observed), and (3) the highest bird nest density occurred at Tivoli North Bay (65 nests ha⁻¹).