Wetland areas are of extraordinary importance for the conservation of wildlife. The Aiguamolls de l'Empordà Natural Park, located in Girona (northeast Spain), is one of the few areas in Europe acting as a way station for migratory birds. The natural park is made up of a brackish water reserve and a fresh water reserve. Agriculture and tourism, which are concentrated especially around coastal population centers, are the main activities in this area and result in the release into the environment of nutrients, pesticides, and heavy metals. This article aims to investigate the presence of nutrients, selected pesticides (organochlorine compounds, permethrin and triazines) and metals (Cr, Cu, Cd, Ni and Pb) in water, sediments, and fish samples. In the case of water, seasonal variations in levels of contamination were also monitored. Comparison was made of the fresh and brackish water reserves and concentration factors for metals and pesticides in sediment were determined. We conclude that the most significant sources of contamination in the natural park are from the entry of pesticides and nutrients into surface waters and sediments as a result of the intensive farming activity of the surrounding areas. The pesticides with the greatest presence were found to be lindane, heptachlor epoxide, permethrin, and atrazine. Among the metals analyzed, Cu and Cr presented the highest concentrations in surface waters and sediments.