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At Batiquitos Lagoon, open water habitat is represented mostly by marine water that is seasonally influenced by freshwater. Freshwater influences are most evident in the eastern basin. During quarterly sampling in 1997, the lagoon was fully tidal (water in the lagoon exchanges fully with the ocean), as indicated by the salinity of the lagoon water, which was similar to the salinity of the ocean (28.10 parts per thousand [ppt] near a drainage in the eastern basin to an October high of more than 34 ppt in all basins).
Looking west across the East Basin
Open water habitat in Batiquitos Lagoon is found in the western, central, and eastern basins, from 0 feet MLLW to the deepest parts of the lagoon. This habitat type is characterized more by its physical characteristics than by the plants and birds that live in it. Based on these physical characteristics, this habitat can be subdivided into three areas:
Salt Water LagoonThe salt water lagoon in Batiquitos Lagoon is 226 acres. Because the lagoon has only recently been reconnected to the ocean, the size and shape of channels on the lagoon floor are still being developed by tidal flows. The small and large channels that have formed in the lagoon are important to the health of the ecosystem because they allow nutrient-rich water and sediment to flow into the lagoon and influence the location of mudflats and other important habitat types. The channels currently follow the regular lines and angles of the dredge cut and propeller scars left on the flats by construction vessels. Where larger channels are forming, erosion is creating gentle meanders and more rounded corners with scoured banks and depositional shoals. In the far eastern basin, a large (5- to 10-foot-wide) channel accompanies the terminal alluvial fan of San Marcos Creek. This channel enters the lagoon along the south side of the E-3 nesting colony. Several small channels are also developing along the mudflats next to the E-1 nesting colony, in the western portion of the eastern basin, and on the more extensive flats of the central basin. With continued tidal flow, these drainage channels will become more precisely defined. Large tidal channels generally are restricted to large mudflats where there is enough drainage area to scour the deep channels. Near ShoreThe near shore is an important part of the Batiquitos Lagoon ecosystem. The daily ebb and flood of the tide provides the lagoon with marine water, a process that exchanges nutrients between the land and the sea. The lagoon is rich in land-generated nutrients and lower trophic-level organisms that enrich the coastal sea waters during the daily ebb tide. The flood tide brings in ocean-borne organisms and nutrients, as well as "refreshed" salt water (i.e., oxygen-rich water with salts and nutrients). Ocean fish enter the lagoon to feed and sometimes reproduce in the protected, food-rich area. Fresh WaterThe most significant sources of fresh water in Batiquitos Lagoon are the two creeks that drain the lagoon watershed: San Marcos and Encinitas Creeks. The construction of San Marcos Dam on San Marcos Creek reduced the size of the watershed from approximately 60 to 30 square miles. Very little fresh water flows into the lagoon, except during storms. Historically, the creeks contributed large volumes of coarse sediment to the lagoon. Currently, the creeks' most important function is to provide a way for nutrients and lower trophic-level organisms, such as fresh water benthos and terrestrial invertebrates, to enter the lagoon food chain.
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