We report on the distribution of contemporary foraminifera in salt marshes in Mission Bay and Carpinteria Slough, Southern California. Combining these data with existing datasets from Seal Beach and Tijuana, we explore the potential for a regional training set to underpin quantitative reconstructions of paleoenvironmental change from foraminifera preserved in salt-marsh sediments. We demonstrate that species’ distributions are highly dependent on elevation, suggesting fossil foraminiferal assemblages here, as in many other regions, are useful depositional elevation indicators. Transfer functions provide predictions from Mission Bay cores with decimeter-scale uncertainties. Nevertheless, interpretation of marsh-surface elevation change is complicated by a complex geomorphic setting and anthropogenic impacts. An abrupt change in elevation in the mid-1700s may be related to lateral spreading of water-saturated sediments during an earthquake on the Rose Canyon fault, suggesting the potential for foraminifera to support new palaeoseismic and sea-level records for the region.