Ten sediment samples from the Crocodile River (Nahal Tanninim), Israel, were analyzed for their foraminiferal abundance and four samples were selected for O, C and Sr isotopic analysis to examine salinity and taphonomic trends. Two biofacies were documented: a Ammonia tepida (59±20% (1σ)) and a Pararotalia spinigera (75±17% (1σ)) dominated assemblage. The distribution of δ18O, δ13C and 87Sr/86Sr values within shell material (foraminifera, ostracods, mollusks, algae) documented salinity trends within the open-ended, micro-tidal estuary with greater certainty than paleontological analysis alone. The isotopic data allowed the isolation of taphonomic trends by determining which taxa were transported from their original context. The calculated salinities from the four samples from the Crocodile River had a distribution that was bimodal with the two groups fitting into a marine or very brackish salinity regime. Most of the taxa followed this trend with measured salinities from the 87Sr/86Sr values in the shell material indicating a relatively stable salinity of <4‰, and with several specimens from an intermediate salinity regime measuring between 4 and 8.5‰. The remainder of the specimens had considerably higher salinities in the range >30‰. The mixture of specimens in the death assemblage from such diverse salinity regimes indicated transport both landward and seaward in the estuary. This methodology shows promise as an environmental indicator in brackish systems when replicate sampling and the analysis of live specimens cannot be undertaken.