Salt marshes occur near the mouths of both Walker Creek and Lagunitas Creek, and smaller pocket marshes occur along much of the northeastern shore. Most of the bay floor is covered by mud bottom with an extensive infaunal community, and much of the mud surface has a microalgal community. Respiration, by contrast, is about equally split between the plankton and benthic communities. This implies that the net ecosystem metabolism of the bay is supported to a significant extent by the import and oxidation of organic matter produced outside the system. We estimate that about half the organic matter supporting net heterotrophy is supplied from land and about half from the coastal ocean.
Water mixing in the bay, predominantly driven by tidal exchange, is slow.
The combination of slow water exchange, net evaporation, and high net heterotrophy in the summer results in water composition being strongly modified from the composition of either the freshwater inflow or the coastal ocean. The bay becomes slightly more saline than the adjacent ocean, dissolved inorganic phosphorus builds up in the water column, and dissolved inorganic nitrogen largely disappears. The phosphorus buildup apparently reflects release of phosphorus during the oxidation of organic matter, while the nitrogen disappearance represents the net effect of denitrification. Consequently, winter water composition largely reflects mixing between runoff and coastal ocean water. During the winter, high-runoff periods characterized by low salinity, the amounts of dissolved carbon, nitrogen, and phosphorus in the water are largely controlled by the physics of water exchange.