Nutrient (N and P), heavy metal (Ni, Cd, Cr, Cu and Pb) and pesticide (DDT, DDD, DDE, lindane, aldrin, endrin, dieldrin, permethrin, atrazine and simazine) concentrations in water and sediment were analysed in the Empordà Wetlands, a Mediterranean wetland area in NE Spain. Mean nutrient and contaminant concentrations and input and output loads via tributaries were compared in two marshes with different water turnover: a freshwater marsh (FWM), with a high water turnover rate due to continuous surface water inputs and outputs, and a brackish water marsh (BWM), with lower turnover and no continuous surface output, where water remains confined during dry periods. Mean concentrations of most heavy metals exceeded the maximum permissible concentration (MPC) in BWM, whilst only some pesticides reached MPC in FWM. The confined waters of BWM showed higher sensitivity to contaminant input loadings than FWM due to the lack of continuous water outputs. Non-point source pollution inputs during runoff (mainly in FWM) and concentration during confinement (mainly in BWM) showed as the main environmental problems related to nutrients and contaminants in these ecosystems. Thus, the importance of confinement and its effect on pollutant concentrations must be borne in mind to achieve correct management of Mediterranean wetlands.