Urbanization of coastal habitats, often exemplified by harbors and marinas, has led to various ecological paradigms, questioning the functioning of these new ecosystems. In the present study we investigated, in a large Mediterranean harbor, whether spatial variation of pollution is present and if this variability drives the structure of the sessile community. We hypothesized locations to have significantly different communities, based on the assumption on the occurrence of environmental gradients of pollution that would constitute selective filters. Three distinct community types were identified in June, coinciding with spatially variable contaminants in sediments. We observed then an unexpected shift of the community between June and August associated to a sharp decrease in biodiversity and a decline of most species, masking the effects of local variation and thus leading to the homogenization of the biodiversity within the harbor. This shift coincided with successive heatwaves (the longest lasting 13 days over 25°C, with a thermal peak at 28°C) which might potentially be associated with a die-off in the harbor communities, regardless of location.