The Saronikos Gulf, an embayment of the Aegean Sea (Greece, Eastern Mediterranean), has undergone profound and unprecedented environmental changes due to the rapid urbanization of the Athens-Piraeus metropolitan area since the 1950s. From the mid-1950s until the mid-1990s, the inner part of Saronikos Gulf was subject to increasing inputs of untreated urban sewage. The resulting long-lasting eutrophication was reflected in the phytobenthos by the presence of low-diversity, mainly ephemeral species communities, largely dominated by the nitrophilous green algae Ulva spp. and Cladophora spp. In the mid-1990s, a wastewater treatment plant started operating on Psittalia islet near the port of Piraeus, capturing the entire central sewage outfall of Athens. Since 1998, the coastal ecosystem of Saronikos Gulf has been under regular monitoring to assess intra-annual and interannual changes in benthic macroalgal communities and nutrient levels. A sharp decline in nutrient and organic loads was soon recorded, leading to a rapid re-oligotrophication of the gulf. Upon this new regime shift, macroalgal communities responded by a general increase in biodiversity and a marked decrease in the abundance of nitrophilous green algae. Within the last years, however, the canopy brown algae (Cystoseira and Sargassum) in the area unexpectedly showed a sharp population decline. Even though this phenomenon may be still ongoing and thus is not fully described and understood, this study is the first to provide a long-term data set of macroalgal responses to a rapid re-oligotrophication process taking place within a highly urbanized Mediterranean coastal area.