Desalination plants along the Mediterranean Israeli coastline currently provide ~587 million m3 drinking water/year, and their production is planned to increase gradually. Production of drinking water is accompanied by a nearly equivalent volume of brine discharge with a salinity of ~80 that is twice the normal, which can potentially impact marine ecosystems. The goal of this study was to examine whether benthic foraminifera, a known sensitive marine bio-indicator, are affected by this brine-discharge. For that, we investigated the seasonal and cumulative effect of brine discharges of three operating desalination facilities along the Israeli coast. Those facilities are located in Ashkelon, Hadera, and Sorek. The brine-discharge in the first two desalination plants is associated with thermal pollution, while the Sorek facility entails increased salinity but no thermal pollution. In four seasonal cruises during one year, we collected surface sediment samples in triplicates by grabs from the outfall (near the discharge site), and from a non-impacted control station adjacent to each study site. Our results highlight that the most robust responses were observed at two out of three desalination shallow sites (Ashkelon and Hadera), where the brine was discharged directly from a coastal outfall and was accompanied with thermal pollution from the nearby power plants. The total foraminiferal abundance and diversity were, generally, lower near the outfalls, and increased towards the control stations. Moreover, changes in the relative abundances of selected species indicate their sensitivity to the brine discharge. The most noticeable response to exclusively elevated salinity was detected at Sorek discharge site, where we observed a sharp decline in organic-cemented agglutinated benthic foraminifera, suggesting that these are particularly sensitive to elevated salinity. The herein study contribute new insights into the effect of brine discharge from desalination plants, on benthic foraminifera, and propose a scientifically-based ecological monitoring tool that can help stakeholders.