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.

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