The distribution patterns of macrobenthic invertebrate assemblages at different spatial scales and in relation to natural and anthropogenic disturbance gradients were investigated in the Pialassa Baiona, a eutrophic and polluted brackish coastal lagoon located along the Italian coast of the northern Adriatic Sea. This coastal lagoon shows a complex physiography with several shallow water ponds and channels separated by discontinuous artificial embankments. Environmental variables and macrobenthic invertebrate assemblages showed higher heterogeneity at small spatial scale (i.e. within channels and ponds). Distinction between channels and ponds is only weakly supported by the distribution patterns of macrobenthic assemblages. Depth was the major factor in structuring benthic communities within ponds, while species distributions along the channels were strongly correlated with the anthropogenic disturbance gradient. Anthropogenic disturbance mainly affected species richness, which was inversely correlated with the organic carbon contents in the sediments and the water surface temperature, which is affected by the input of cooling water from two thermal power plants. Some opportunistic species, like the polychaetes Streblospio shrubsolii and Capitella capitata, were more abundant in the southern polluted areas. In particular, the abundance of S. shrubsolii significantly increased with organic carbon contents in the sediments and water surface temperature, while C. capitata was more abundant in the warmed sites and close to sewages. Conversely, the abundance of the amphipod Corophium insidiosum was inversely related to organic carbon contents.