Late Pleistocene to Middle Holocene sea level rise resulted in a number of changes to coastal ecosystems around the world, providing new challenges and opportunities for coastal peoples. In California, glacial to interglacial sea level rise resulted in some reductions in kelp forest area, but also in the formation of estuaries. Estuaries were important for terminal Pleistocene peoples in the Santa Barbara Channel region (SBC), a pattern that persisted through the Early-Middle Holocene, and sometimes later. While paleoestuaries appear to have been relatively common along the SBC mainland coast, they were rare to absent on the Channel Islands. The Abalone Rocks Paleoestuary on Santa Rosa Island is the only well documented island estuary. However, questions remain about the size and productivity of this estuary and its importance for human subsistence and settlement relative to the more extensive mainland estuaries. Faunal data from two previously unreported sites and synthesis of shellfish data from other Abalone Rocks sites and similarly aged sites near mainland estuaries illustrate the importance of SBC mainland versus island estuaries. Estuarine shellfish were considerably more abundant at Early and Middle Holocene mainland sites, with the Abalone Rocks Paleoestuary largely supplementary to rocky shore habitats. At island estuary sites, taxonomic richness was fairly consistent during the Early-Middle Holocene, although diversity and evenness decline slightly through time, with estuarine shellfish largely disappearing from island assemblages prior to 5000 years ago. These data demonstrate the power of archaeological research to evaluate the relationships between past environmental change and human behavior.