Coastal lagoons are highly productive systems and the quantification of mass fluxes, which is of paramount importance for the sustainable management of these systems, remains poorly studied. In this context, a detailed study was conducted to better understand the exchanges between the productive coastal lagoon Ria Formosa (South-West Europe) and the ocean. The exchanges of water, nutrients, chlorophyll-a and suspended solids between the main inlets (Faro-Olhão inlet - BFO; Armona inlet - BAR; and Ancão inlet - BAN) and adjacent channels (Faro - CF and Olhão - CO) and the adjacent ocean were estimated along complete semidiurnal tidal cycles, under extreme fortnightly tidal ranges and different seasonal and environmental/oceanographic conditions. The net tidal prism was highest during spring tides. Among the three inlets, BFO was the most important in terms of exchange, followed by BAR and BAN. Net transport at BFO was lowest during the Summer campaign, although it exported material that fertilised the adjacent coast. The persistent net export of suspended solids and ammonium suggests the higher biological productivity of Ria Formosa compared to that found in coastal waters. In the Winter campaign, after a period of rainfall and increased land runoff, there was a remarkable export of matter, on which, ammonium and suspended particles exported can exceed 0.3 times and almost 0.9 times, respectively, those imported from coastal water. However, the import of phosphate and nitrate can be attributed to a weak coastal upwelling event, as well to low consumption and nitrification at this period of low temperature. During the Spring and Autumn campaigns, the Ria Formosa was fertilised either by upwelling events or due to rapid consumption of nutrients by phytoplankton in this shallow system. BFO and the other two inlets of the western sector of Ria Formosa are interconnected by CF and CO. The higher nutrient transport was recorded at CF, despite the highest nutrients concentrations was recorded at CO. The data show the strong link between physical and biogeochemical processes with meteorological/oceanographic factors. The study showed that associated biological processes are superimposed on the tidal effect in this system. Data from this study could be used as a reference, particularly important for management of Ria Formosa, a productive system where bivalves production depends deeply on water quality. In addition, the nutrient concentrations and mass exchanges resulting from the different processes can be used as a reference for other lagoon systems where shellfish production is practised.