Environmental quality in nearshore marine/estuarine environments can vary both spatially and temporally due to changes in natural and anthropogenic influences. This is especially true in the Gulf Coast, where human development often occurs adjacent to “nursery” habitats critical to fishing industries. Benthic foraminiferal assemblages can provide a valuable index of “short-term” and “time-averaged” environmental conditions. This report is part of an on-going Florida Geologic Survey research project to map salinity and water quality in sensitive coastal areas adjacent to offshore fresh water springs. The focus of our research is to investigate using benthic foram assemblages to track water quality, in particular salinity near springs and pollution near suspected sewage outfalls. Initial efforts have been focused on Spring Creek, estuarine location of several major springs, and St. Joseph Bay, a shallow restricted embayment surrounded by housing and industry. In both areas, surface sediment samples (along with various physical parameters) from a variety of locations are processed for both living and dead foram specimens. Species distributions are evaluated statistically and the effects of temperature, depth, and sediment grain size are minimized. Initial results suggest that foram specimen density, foram assemblage diversity, and absolute/relative abundances of several forams, especially Ammobaculites species, make excellent indices of salinity in the range 4-13 ppt. Similar patterns have emerged for analyses of samples affected by human effluent.