The San Francisco Estuary is a young estuary, about 6-10,000 years old in its present location. It became established during periods of high climatic variability (reflected in extreme floods and long droughts) compared to the relatively stable past 150 years. The Delta was formed as a huge freshwater marsh through the interaction of river inflow and the slow rise of sea level with the growth and decay of tules and other plants. This interaction resulted in the deposition of large amounts of organic matter, creating layers of peat that kept pace with sea level rise. These peat layers formed the soils of most of the present Delta ‘islands’, which were actually complex patches of floodable marsh.
The channels among the islands were historically shifting, winding distributaries of the entering rivers that moved inflowing water through the Delta, providing access to upstream areas for large runs of migratory fish. The movement and quality of water in these channels was strongly affected by tidal action. These attributes also created a complex of diverse and shifting habitats that supported a wide variety of functions for an ecological system in which there was no clear separation between aquatic and terrestrial components.