This study aimed to assess the influence of treated wastewater disposal on Ria Formosa coastal lagoon (South Portugal), the largest national producer of bivalve mollusks. Water quality was evaluated at two areas under different wastewater loads and hydrodynamic conditions, using physico-chemical variables, bacterial indicators of contamination, chlorophyll-a concentration, phytoplankton abundance and composition. Samples were collected monthly, between October 2018 and September 2019. Minor influence of effluent discharge was detected at the eastern Olhao ˜ area, exposed to stronger hydrodynamics and higher wastewater load than the northwestern Faro area (ca. 2–4-fold total nitrogen and phosphorus). The lower load weakly flushed area showed a poorer water quality, up to 500 m from the discharge point, more marked during the spring-summer period. The intensity, persistence, and spatial extent of the wastewater footprint, lower for the highest-loading area, reflected the role of local hydrodynamic conditions, modulating the influence of wastewater discharge on lagoonal water quality. | MAR-01.04.02-FEAMP-0003 | info:eu-repo/semantics/publishedVersion