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Small, temporally dynamic and biologically diverse wetlands are among the most endangered ecosystems. One of the major causes of wetland degradation is agricultural practices specially pollution. However, agriculture is one of the major economically relevant human activities in the Mediterranean area. The European Commission has a great interest in transforming agriculture in a more sustainable activity, which will improve the regional development especially in rural areas. Re-connecting farmers with the agroecosystem through a sustainable framework is necessary in order to protect specifics ecosystem such the wetlands that are surrounded by intensive agriculture. There is a lack of specific assessment tools and indicators to such ecosystems despite their significant contribution to aquatic biodiversity. In order to develop a more sustainable management of wetland watersheds, their risk characterization should be evaluated and the strategies to conserve or restore them should be encompassed to the activities developed on them.