Marine environment of the Arabian Gulf is naturally stressed due to marked fluctuations in sea temperatures and high salinities. Anthropogenically induced stresses including waste water discharges from desalination plants could pose additional threats to the coastal and marine ecosystems in the Arabian Gulf. Macrobenthic assemblages in the proximity of two major desalination plants that use Multi-Stage Flash (MSF) and brackish water Reverse Osmosis (RO) technologies in Bahrain were investigated. Reduced levels of biodiversity and abundance were recorded in sampling stations adjacent to the outlet of MSF reflecting severe impacts on macrobenthic assemblages caused by brine effluents that associated with high temperatures, salinities, and a range of chemical and heavy metal pollutants. Although localized severe impacts on macrobenthic assemblages were detected, collective discharges of desalination effluents, may synergistically contribute to the degradation of the naturally stressed marine ecosystems and natural resources in the Arabian Gulf.