The aim of this study was to evaluate the water quality of the Cértima River basin (Central Portugal). For that purpose, surface water samples were collected in March, May and July 2003, at 10 selected sampling sites, and were analysed for physicochemical parameters, namely temperature, conductivity, pH, total suspended solids, dissolved oxygen, biochemical oxygen demand (BOD5), Kjeldahl nitrogen and total phosphorus. Results revealed an acceptable water quality during the spring season. Maxima of 64 mg dm−3 for BOD5, 39 mg dm−3 for Kjeldahl nitrogen, and 5.2 mg dm−3 for total phosphorus, were recorded during summer, indicating a significant degradation of the water quality in a river stretch located downstream of the town of Mealhada. These values, which did not comply with the objectives of minimum quality for surface waters prescribed by the Portuguese legislation, were related to domestic wastewater discharges and runoff waters from a cattle farm. Besides their effects on the middle stretch of the river, these pollution sources were the most likely cause of the high nutrient load in downstream waters, and thus may have a major impact on the trophic status of Pateira de Fermentelos, a sensitive wetland area located in the lower Cértima basin.