Agriculture is a major source of diffuse pollution, where nitrogen and sediment pollution of water bodies are its main associated environmental impacts. Best management practices are effective tools for preventing and minimizing water pollution. Water quality models and model-based scenario analyses are useful tools for assessing impacts of best management practices and to identify appropriate strategies on the watershed scale. This study was conducted in the southernmost Mar Menor basin, one of the largest saltwater coastal lagoons in Europe and threatened by diffuse nutrient and sediment export from the agricultural landscape. This study evaluates the impact of several management practices on nitrogen and sediment loads, and horticultural crop yield, to identify an appropriate management strategy on the watershed scale. Both structural and nonstructural management practices scenarios were evaluated: three scenarios representing field operations, two coastal line buffers, a new fertilizer management strategy and a change in the productive cultivation system from three-crop rotation to two-crop rotation. Each management practice reduced a certain type of diffuse pollution and, therefore, a combined set of changed management practices is necessary to cope with all agricultural pollution types. Contour farming, combined with hedgerow field borders, was effective in sediment yield and surface organic nitrogen export reduction terms, while improved fertilizer management reduced surface nitrate export and leaching with minimal impacts on crop yields.