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. The classification system distinguishes between intertidal and subtidal habitats, since biological communities often differ significantly according to the degree of tidal influence. Special adaptations are required by intertidal species to resist desiccation and tolerate large variations in temperature and salinity associated with tidal exposure. Subtidal habitats are below extreme low water, and thus have continuously submerged substrates. Intertidal habitats are exposed and flooded by tides as often as twice daily or as seldom as a few times a year.