Since it is influenced by both the marine and the riverine systems, bay sediments are primarily a mixture of coarse marine sands and fine river-borne silts and clays. Salinities during the summer are moderate to high, depending on the basin size, but may vary considerably with tidal stage and freshwater flow. Most bays have a wide diversity of habitats with extensive intertidal flats, eelgrass beds, algal beds, and marshes. The riverine subsystem includes the upper tidewater portions of the larger tributaries which enter the estuary. A large percentage of the subsystem is narrow, subtidal river channel.
Current velocities exhibit dramatic seasonal changes which influence benthic communities.
Salinities are low most of the year, and portions of the subsystem may be entirely fresh water. Sediments range from fine silts and clays to cobble and gravel. The slough subsystem is a sheltered environment, which is usually a narrow, isolated arm of the estuary with a very limited freshwater flow from uplands. Salinity is influenced by the proximity of the slough to the estuary mouth. Sloughs usually have fine organic sediments and high percentages of intertidal land consisting of flats, eelgrass beds, and marshes.