Understanding the natural spatial and temporal variability that exists within an ecosystem is a critical component of efforts to restore systems to their natural state. Analysis of benthic foraminifers and molluscs from modern monitoring sites within Florida Bay allows us to determine what environmental parameters control spatial and temporal variability of their assemblages. Faunal assemblages associated with specific environmental parameters, including salinity and substrate, serve as proxies for an interpretation of paleoecologic data. The faunal record preserved in two shallow (