Benthic foraminifera were sampled in Rehoboth Bay, Atlantic coast of Delaware (USA), to evaluate the use of canonical correlation on foraminiferal distributions, and the applicability of stable isotope analyses to track the relative proportions of fluvial versus marine inputs to the sediment-water interface. Canonical correlations indicate that water depth, bottom-water dissolved oxygen (D.O.) levels, temperature, and salinity are the principal environmental factors related to the distribution of foraminifera in the bay. There are five dominant species in the bay fauna; in order of decreasing abundance, they are Ammonia tepida, Elphidium poeyanum, E. excavatum, Haynesina germanica, and Ammotium salsum. The canonical analysis shows that Elphidium excavatum and Haynesina germanica have the strongest response to salinity, with the former species favoring higher values and the latter species favoring lower ones. The importance of salinity is apparent in the stable isotopic composition of Ammonia tepida and Elphidium poeyanum, which yield δ18O values that are lowest at the sites closer to the freshwater input and increase with distance from it. The relationship between δ18O values and salinity for both stained and unstained tests is statistically significant (P < 0.05). With respect to temperature, only the δ18O values of unstained (non-living) specimens also correlate with temperature. These results suggest that faunal patterns and the stable isotopic composition of these foraminiferal species reflect mixing of marine and fresh waters in this bay. The faunal and geochemical approaches could provide a means to trace fresh versus seawater mixing from core samples.