During their operation, seawater thermal desalination plants may adversely affect aquatic communities in estuaries by the impingement of organisms on intake screens, the entrainment of various life forms in cooling water systems, the thermal and brines loadings of receiving waters with the release of harmful components containing heavy metals (Cu, Fe, Ni, Cr, Zn), additive substances (anti-scaling, antifouling, antifoaming, anticorrosion) and their conversion products. Desalination plant discharges influence both the water quality and the organisms of impacted estuaries, directly or indirectly with the most acute effects found in the vicinity of the discharge outfalls outlet. Increasing temperature lowers the dissolved oxygen content of receiving waters while raising the metabolism rate of its faunal inhabitants, elicit physiological and behavioural responses in organisms. An increase in salt concentration, which raises the density of waters, fosters stratification of receiving water bodies, can lead to an increase of turbidity, disrupt the photosynthesis process, and disturb the biogenesis, to an extinction of mainly sensitive benthic species, larvae and young individuals. Some of the chemical components released by desalination plants pose a potential hazard to estuarine organisms owing to their toxicity. Most important in this respect are chlorine and trace metals loads which must receive much attention because at times it accounts for much of the mortality of susceptible organisms in discharge waters, leaving their mark on the flora and fauna around the pipeline outlet. The ultimate consequences on estuarine communities of all these physical and chemical parameters of these discharges are shifts in their structure. Changes in species composition, species diversity, and population density are commonly observed in the area of the discharge. In some cases, opportunistic or nuisance species may replace equilibrium populations at heavily impacted sites.