Designated in 1991, CBNERRVA established a multi-component system along the salinity gradient of the York River estuary that encompassed the diverse collection of habitats found within the southern Chesapeake Bay subregion. With its two principal tributaries, the Pamunkey and Mattaponi Rivers, the York River is the Bay's fifth largest tributary in terms of flow and watershed area. The York River estuary is classified as a microtidal, partially mixed estuary. Tidal range varies from 0.7 m and at its mouth to over 1 m in the upper freshwater tributary reaches and salinity distribution ranges from tidal freshwater to polyhaline regimes. Land use is predominantly rural in nature with forest (61%) and agricultural lands (21%) being the dominant land cover; wetlands comprise approximately 7% of the basins area. Reserve components include: (1) Goodwin Islands (148 ha), an archipelago of polyhaline salt-marsh islands surrounded by inter-tidal flats, extensive submerged aquatic vegetation beds, and shallow open estuarine waters near mouth of the York River; (2) Catlett Islands (220 ha), consisting of multiple parallel ridges of forested wetland hammocks, maritime-forest uplands, and emergent mesohaline salt marshes; (3) Taskinas Creek (433 ha), containing non-tidal feeder streams that drain oak-hickory forests, maple-gum-ash swamps and freshwater marshes which transition into tidal oligo and mesohaline salt marshes; and (4) Sweet Hall Marsh (443 ha), an extensive tidal freshwater-oligohaline marsh ecosystem located in the Pamunkey River, one of two major tributaries of the York River. CBNERRVA manages these reserves to support informed management of coastal resources by supporting research that advances the scientific understanding of watershed and estuarine systems, highlighting proper stewardship of coastal resources, and improving general public and professional literacy through education and training programs.

The four separate sites of the Chesapeake Bay National Estuarine Research Reserve in Virginia are within the Coastal Plain province of the mid-Atlantic. The surficial geology at each site is of Quaternary age, primarily Holocene wetlands. The site at Taskinas Creek is set into Tertiary age strata. The underlying strata increase in age up-stream. Regionally, the Late Tertiary and Quaternary geology is a function of the series of major transgressions and regressions, during which the successively more recent high stands of sea level generally have not reached the level of the preceding high stand. As a consequence, stratigraphically higher, younger deposits occur topographically below exposures of the older strata. The two down-stream reserve sites are within the area of the Eocene age Chesapeake Bay Impact Crater. Also at these two sites, the tidal marshes are superimposed on a ridge and swale topography. The local rate of sea-level rise, approximately 4 mm/yr, is the underlying process driving changes to the tidal marshes at all four sites. The Goodwin Islands, at the mouth of the York River with exposure to Chesapeake Bay, can be severely impacted by storm waves and surge. Future research should include a program ofcoring to develop the time-history of recent rise of sea level and assist on-going efforts toward mapping the regional geology and toward understanding the local and regional ground-water systems.In addition, establishment of permanent benchmarks to document elevation would enable long-term monitoring of subsidence and facilitate differentiation of the eustatic and isostatic components of changes in relative sea-level rise relative to climate change or other factors.

The York River is a partially-mixed, microtidal estuary with tidal currents in the mid- to upper estuary approaching 1 m/s. The upper York near West Point is generally less stratified than the lower York near Gloucester Point because of the shallower depths and stronger currents found upstream. Fluctuations in salinity stratification in the York River at tidal, fortnightly and seasonal time-scales are associated with tidal straining, the spring-neap cycle, and variations in freshwater discharge, respectively. Estuarine circulation in the York River, which averages ~5 to 7 cm/s, is often modulated by moderate winds. Waves are usually insignificant, although occasional severe storms have a major impact. The York River channel bed is predominantly mud, while the shoals tend to be sandier, and the mid- to upper York is marked by seasonally persistent regions of high turbidity. Fine sediment is trapped in high turbidity regions in response to tidal asymmetries and local variations in stratification and estuarine circulation. More work is needed to better understand the linkages between physical oceanography, sediment transport and turbidity in the York River system, especially during high-energy events and in response to ongoing climate change.

Key water quality management issues and threats within the Chesapeake Bay and its tidal tributaries include excess loadings of sediment and nutrients, and the introduction of toxic chemicals and microbial agents. Poor water clarity, principally controlled by suspended sediments and phytoplankton, is a persistent and widespread problem in the York River estuary with the oligohaline and middle mesohaline regions failing to meet submerged aquatic vegetation (SAV) habitat requirements (SAV criteria: ~10 NTU and TSS < 15 mg L⁻¹). Both the primary and more localized secondary estuarine turbidity maximum are associated with these regions where elevated surface (30–35 mg L⁻¹) and bottom (80–105 mg L⁻¹) water TSS levels are observed. While nonpoint agriculture sources dominate riverine sediment load inputs, tidal and nearshore erosion are a significant source of suspended sediment in the York River estuary. As with sediment, nonpoint agricultural sources dominate nutrient inputs and streamflow is a dominant controlling factor in explaining variability in annual loads. Within mainstem surface waters, TDN and TDP concentrations exhibit a decreasing trend with increasing salinity. TDN and TDP concentrations are on the order of 40–45 μmol L⁻¹ and 1.2 μmol L⁻¹, respectively, in the tidal freshwater reaches of the Pamunkey and Mattaponi Rivers and 22–24 μmol L⁻¹ and 0.6 μmol L⁻¹ in the polyhaline regions of the York River. Mean DON exhibits little variation between salinity regimes. Seasonal phytoplankton biomass and productivity vary between salinity regimes with mean monthly peak chlorophyll a concentrations on the order of 9–10 μg L⁻¹ in the tidal freshwater reaches, 14–18 μg L⁻¹ in the transition zone below the freshwater region, 25–28 μg L⁻¹ in the upper and middle mesohaline reaches, and 15 μg L⁻¹ in the lower mesopolyhaline region. Based on DIN:DIP molar ratios and limited nutrient enrichment studies, tidal freshwater regions experience year-round phosphorus limitation, shifting to seasonal nitrogen limitation in the lower oligo, meso and polyhaline regions of the York River. Harmful algal bloom (HAB) producing dinoflagelletes have resulted in “red tides” that generally occur annually (summer, early fall) in the lower York River. With respect to low dissolved oxygen levels, hypoxia derived from oxidation of organic matter and sediment oxygen demand has also been observed repeatedly in the bottom waters of the lower, high salinity reaches when water temperatures exceed 20 °C. While studies have indicated limited toxic chemical contamination, mercury and PCB fish consumption advisories and restrictions have been issued within the York River estuary. Mercury impacted regions of the Mattaponi and Pamunkey Rivers receive significant wetland drainage that can enhance the potential for bioaccumulation of mercury in fish. Sediments in the York River proper exhibit PCB levels ranging from 1–5 ppb with more elevated levels (25 ppb) being observed in some contributing tidal creeks. In contrast to mercury where atmospheric deposition is a primary pathway, PCBs are generally released into the environment from runoff processes occurring at hazardous waste sites. With varying sources of fecal pollution, 20 percent (31.1 km²) of the York River's assessed shellfish waters has been designated as impaired. Condemned waters are restricted to major industrial and defense facility sites, and contributing smaller tidal creek systems.

The York River has nine tidal wetland community types that are distributed along gradients of salinity and tidal inundation. These range from the Saltmarsh Cordgrass community dominated by Spartina alterniflora to the Tidal Freshwater Mixed community that can have over 50 species in one marsh. These tidal marshes provide a number of important functions and values to the estuarine systems including: high primary productivity, important habitat value, erosion buffering and filtering capacity useful for trapping sediments, pollutants and nutrients. The tidal marsh communities within the four Chesapeake Bay Virginia National Estuarine Research Reserve sites are situated along the York system in polyhaline, mesohaline, oligohaline and freshwater salinity regimes. They are largely pristine vegetation communities and have been documented to have abundant fauna characteristic of their individual community types. Changes in the vegetation communities of each site have been documented over time; however more research is needed on the potential effects of projected sea level rise on these habitats and the roles of watershed sedimentation and nutrient enrichment, vegetation succession, and invasive species on the persistence and value of these tidal marsh areas.

Submerged aquatic vegetation or SAV are important components of shallow water areas of the York River estuary. The plants that comprise these communities are distributed in shallow water areas (<2m) along the estuary from polyhaline to freshwater areas according to their individual salinity tolerances. Eelgrass (Zostera marina) is the only true seagrass and is found only in the lower York River where salinities average above 20 psu. It is a cool water species that decreases in abundance in the summer due to high water temperatures. SAV in this region have declined precipitously from historical abundances due to excessive levels of turbidity and nutrients. Infection of a marine slime mould-like protist, Labyrinthula zosterae, also impacted this species in the 1930s, nearly decimating it from this area. Widgeon grass (Ruppia maritima) co-occurs with eelgrass but can also grow in low salinity areas. Pondweeds (Potamogeton) and many other SAV species grow in both low salinity and freshwater areas. Macroalgae or “seaweeds” are currently a minor component of SAV in the York River system. Several algal genera common in the area include: Agardhiella, Ulva, Enteromorpha and Chara. While there has been a great deal learned through research and monitoring relative to SAV communities in the Chesapeake Bay, in general, and the York River, in particular, more efforts are needed to advance SAV protection and restoration to achieve the SAV restoration goals. Research efforts are needed to further understand the relationships between environmental conditions and SAV response and the interactions between of various stressors on SAV. Other areas for further research focus include investigations of the relationships between natural and restored SAV growth, survival and bed persistence and biological stresses including herbivory or secondary physical disturbance through foraging, bioturbation or other activities. One important need is to quantify the short and long term relationships between SAV decline and recovery and climatic factors such as storms, droughts, and temperature extremes that may be influenced by climate change.

The York River possesses a diverse phytoplankton community represented by a variety of algal species that includes both freshwater and estuarine flora. The mean annual monthly range of abundance is ca. 5–20 X 10⁶ cells L⁻¹ with an extended bi-modal pattern that begins with an early spring diatom peak (March) that declines into early summer. The development of a more diverse representation of taxa in the summer results in a secondary late summer-early fall peak. Diatoms are the dominant phytoplankton component throughout the entire estuary including a variety of pennate and centric species such as Asterionella formosa and Aulacoseira granulata. Dinoflagellates are more common and abundant in the lower segments of the York River where they have been associated with re-occurring and extensive “red tide” blooms. These include Cochlodinium polykrikoides, Heterocapsa triquetra, Heterocapsa rotundata, Scrippsiella trochoidea, and Prorocentrum minimum. Cynobacteria, commonly referred to as blue-green algae, include unicellular, colonial, and filamentous taxa that are predominantly freshwater species. Among the more common taxa are Microcystis aeruginosa, a potential bloom producer, Merismopedia tenuissima, Oscillatoria spp., Dactylococcopsis spp., Chroococcus spp. and Synechococcus spp. The cyanobacteria are generally considered a nuisance category that do not represent a favorable food resource, and are commonly associated with increased trophic status. Chlorophytes or green algae, including Ankistrodesmus falcatus, Chlorella spp., Pediastrum duplex, Scenedesmus acuminatus and Scenedesmus dimorphus are more common from spring to fall with lowest abundance in winter. Overall, the phytoplankton status in the York has been classified as poor/fair condition. Further studies are needed regarding interrelationships between the floral and faunal components of the plankton community and linkages to water quality and physical environmental factors in the system. In addition, continued observations regarding long-term trends in phytoplankton abundance and composition need to be followed with emphasis on any increasing presence of potentially harmful phytoplankton species.

Zooplankton are a diverse group of heterotrophic organisms that consume phytoplankton, regenerate nutrients via their metabolism, and transfer energy to higher trophic levels. Over the past 40 years, few studies have specifically targeted zooplankton communities of the York River estuary and tributaries. However, several studies targeting specific taxa, and time series of multiple taxa, provide an emerging view of York River zooplankton community composition and how zooplankton communities change seasonally, and over longer time scales. Microzooplankton communities are dominated by ciliated protozoa, and rotifers are important in fresher water regions. In the lower Bay microzooplankton abundance peaks in spring, and in mid-summer to early fall. The mesozooplankton community is dominated by calanoid copepods Acartia tonsa, Acartia hudsonica, and Eurytemora affinis. Mysids undergo diel vertical migrations and are important food for many fish species in the Bay. Some taxa such as chaetognaths are not endemic to the bay but are transported in from the continental shelf. Various meroplankton such as larvae of decapods, bivalves, and gastropods become abundant at times. A striking seasonal change in the zooplankton community composition occurs in spring when large gelatinous zooplankton such as the ctenophore Mnemiopsis leidyi and (subsequently in summer) the scyphomedusa Chrysaora quinquecirrha (sea nettle) “bloom.” Mnemiopsis blooms now appear earlier in the York River compared to 40 years ago, correlated to earlier warming in spring water temperatures. Humans may be influencing zooplankton populations in the York River via introduced species and eutrophication-induced hypoxia, as well as via input of contaminants. Future research priorities and monitoring needs include long-term monitoring of zooplankton communities, increased studies of the dynamics of microozooplankton and of gelatinous zoopankton, diel and seasonal cycles and grazing rates of some of the lesser studied groups (e.g., other than copepods), and use of new technology such as underwater digital video systems.

Benthic organisms and their communities are key components of estuarine systems. We provide an overview of the biology and key ecological features of benthic communities of York River Estuary (YRE), which is the site of the Chesapeake Bay National Estuarine Research Reserve in Virginia (CBNERRVA). Major subtidal benthic habitats in YRE include soft mud and sand bottoms, with only limited distribution of submerged aquatic vegetation and oyster shell. Major taxonomic groups of macrofauna dominating muds and sands of YRE include annelids, molluscs and crustaceans; similar to those found in other temperate estuaries of the US Mid-Atlantic. Meiofaunal assemblages of YRE soft bottoms are dominated by nematodes and copepods. Species distribution patterns in YRE are strongly correlated with salinity and bottom type, while other factors such as eutrophication and hypoxia may be growing in importance. Much of the YRE benthos fails to meet the restoration goals set by the Chesapeake Bay Program. The poor condition of the benthos is expressed as low biomass and abundance and may be associated with degraded water quality, hypoxia and sediment disturbance processes. No comprehensive inventory of the benthic biota of the CBNERRS sites is available, which will make it difficult to assess future changes due to human impacts such as climate change or the introduction of exotic species. Given this paucity of data, a systemic cataloging of the benthic resources of the reserve sites and any potential invasive species is a much needed avenue of future research for CBNERRVA.

The York River system supports a diverse fish fauna represented by members of the shad and herring family, drums, flatfishes, temperate basses, catfishes, sharks, skates, rays, and numerous smaller fishes that serve as forage such as bay anchovy, Atlantic menhaden, and killifish. Historically, fisheries for blue crabs, American shad, striped bass, and Atlantic sturgeon thrived in the Chesapeake Bay region but in recent times, and with the exception of striped bass, these fisheries have declined. Fishes of the York River exhibit divergent life history patterns, from fast growing, highly fecund species such as alewife, to slow growing, late-maturing species with low fecundity such as Atlantic sturgeon. The young of many species use the York River system as a nursery area and depend on the high productivity of this estuary for conferring fast growth and high survival during the first year of life. Habitat alterations that result in loss of water quality or quantity may deleteriously affect recruitment of young fishes through direct effects on young-of-the-year fish survival, or through disruption of spawning activity (e.g., dam construction, and water withdrawals that affect salinity and flow). Continued monitoring of recruitment success is crucial to understanding population-level responses to environmental and human-induced perturbations, especially in light of the projected growth of the human population in this watershed. Other important areas of continued research include assessment of habitat use and delineation of trophic interactions.

The York River and its watershed support many natural vegetative communities, from aquatic grass beds to tidal marshes to a variety of woodlands. These communities support a wide variety of resident and migratory amphibians, reptiles, birds and mammals. There are eight families and 26 species of amphibians and ten families and 36 species of reptiles represented within the York River watershed. All three species of sea turtles are protected under the Endangered Species Act and the Northern diamond-backed terrapin is a species of concern. Approximately 230 bird species, resident and migratory, have been recorded within the Chesapeake Bay area. Over 50 families and 190 species of birds have been observed along the estuarine environments of the York River. Specific Reserve components support Bald Eagle nests and Great Blue Heron rookeries. Nineteen families and 50 species of mammals are represented within the York River and its watershed. Of special note is the infrequent occurrence of large marine mammals, such as the bottlenose dolphin and manatee, within the lower York River region.

The overall goal of the Chesapeake Bay National Estuarine Research Reserve in Virginia (CBNERRVA) research and monitoring program is to promote, coordinate and conduct research and monitoring to enhance the scientific understanding and management of the York River and southern Chesapeake Bay coastal ecosystems. The regions of greatest scientific emphasis are located within four Reserve sites located along the York-Pamunkey River estuarine system. Primary research and environmental monitoring areas include: estuarine and shallow water environments including benthic communities, submerged aquatic vegetation and emergent wetlands habitats, open water regions and adjacent watersheds and air sheds. Both national priority (NOAA) and Chesapeake Bay specific (Chesapeake Bay Program) research focus areas are pursued within the Research Reserve with goals to: enhance scientific understanding of coastal ecosystems, surrounding environments and the natural and human processes influencing such systems; and, promote the effective management and conservation of natural and cultural coastal resources through informed decision-making. A System-wide Monitoring Program (SWMP) initiated by the Estuarine Reserves Division (ERD) of NOAA provides standardized data on national estuarine environmental trends through similar measurements of abiotic and biotic variables as well as watershed and land use classifications and measurements at each of the 27 Reserves. Data are compiled electronically at a central data management location and are available via web interface ( www.vecos.org). Ongoing York River monitoring programs at the CBNERRVA reserve sites include; meteorological and streamflow monitoring, water quality monitoring and biological monitoring are available through the Reserve or via web interface. Multi-parameter water quality, in situ monitors at both fixed and buoyed stations, point sampling and continuous underway flow-through monitoring form the basis of the water quality monitoring program. Research opportunities at Reserve sites are available to any qualified scientist, academician or student affiliated with a university, college or school, non-profit organizations, and non-academic research institutions. In addition, the Reserve sponsors competitive graduate research fellowships through the NERRS Graduate Research Fellowship (GRF) Program for student research in the York River system.