Salinity is a measurement of the concentration of solids dissolved in water and is measured in parts per thousand (ppt). Estuaries are bodies of water where tidal action brings seawater (~35 ppt) to mix with freshwater (0-0.5 ppt) from rivers and streams. Dry/wet climates can also influence salinity. The salinity of the water affects the distribution, growth and disease resistance of seagrasses.

Eelgrass, Zostera marina, prefers polyhaline waters, or estuarine waters with salinities ranging between 20-31 ppt. At low to intermediate salinities (10-20 ppt) eelgrass can survive, continuing to photosynthesize, but productivity is reduced by 50%. The onset and severity of wasting disease, a pathogen infecting eelgrass, has been linked to these intermediate salinities when eelgrass is stressed. Also, germination of eelgrass seeds is stimulated at low salinities.

Long Island's Estuaries (learn more...) include the Peconic Estuary, the South Shore Estuary, Long Island Sound, and the Hudson/Raritan Estuary. In the Peconic Estuary, salinities range from about 9 ppt at the mouth of the Peconic River to about 30 ppt in Gardener's Bay. The South Shore Estuary Reserve, including Shinnecock Bay, Moriches Bay, Great South Bay, and Hempstead Bay, has varying salinities depending on the distance to the inlet. The salinity of Long Island Sound averages between 27 and 32 ppt, but varies depending on proximity to freshwater tributaries, and generally there is a gradient of increasing salinity from west to east. Salinity in the Hudson Raritan Estuary, including Raritan, New York, Newark and Jamaica Bay Complexes, also depends on proximity to the freshwater tributaries which includes the Hudson River.

When estuarine waters don't mix well, a stratification can occur due to the different densities of fresh and salt water. Since saltwater is about 3.5% salt (a.k.a. 35 ppt), it is more dense than freshwater, which can cause a vertical gradient or layering, known a a halocline.

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