Desalination is a growing activity that has introduced a new impact, brine discharge, which may affect benthic communities. Although the role of polychaetes as indicators to assess organic pollution is well known, their tolerance to salinity changes has not been examined to such a great extent. The aim of this study was to examine the effect of brine discharge over soft bottom polychaete assemblage along the Alicante coast (Southeast Spain) over a two year period. Changes in the polychaete assemblage was analysed using univariate and multivariate techniques. We compared a transect in front of the discharge with two controls. At each transect we sampled at three depths (4, 10 and 15 m) during winter and summer. We have observed different sensitivity of polychaete families to brine discharges, Ampharetidae being the most sensitive, followed by Nephtyidae and Spionidae. Syllidae and Capitellidae showed some resistance initially, while Paraonidae proved to be a tolerant family.