The discharge of an effluent of high salinity from reverse osmosis desalination plants has a strong impact on marine communities. The aim of this study was to examine the effect of brine discharge over soft bottom communities along the Alicante coast (Southeast Spain) over a two year period. Changes in the infaunal assemblage were analysed using univariate and multivariate techniques. Each year we sampled along three transects at three depths (4, 10 and 15m) during winter and summer. We observed a substitution of a community characterized by the presence of Polychaeta, Crustacea and Mollusca, for another dominated by nematodes (up to 98%), in the stations closer to the discharge where salinity values exceed 39 psu.