The significance of nutrient inputs at the watershed scale is best expressed in terms of in-stream processes, compared to evaluating simple field measurements of nutrient inputs. Modeling tools are necessary to consider the complexity of river networks in the determination of the sources and processes by which nutrients are transported at the watershed scale. Mediterranean rivers are potentially vulnerable to climate change (decrease in precipitation and increase of extreme events), and identifying and quantifying nutrient pollution sources and their spatial distribution can improve water resource management at the watershed scale. We apply a hybrid process-based and statistical model (SPARROW, spatially referenced regression on watershed attributes) to a largely disturbed Mediterranean watershed in NE Spain in order to estimate the annual nitrate and phosphate loads reaching the drainage network. The model emphasized the contribution of in-stream processes in nutrient transport and retention, and the inter-annual (7years) effects of hydrological variability on the export of nutrients from the landscape to water bodies. Although forest and grassland land cover types predominate, agricultural activities and human agglomerations were significant sources of nutrient enrichment. Nutrient flux apportionment was also linked to inter-annual hydrological variability. Exported nutrient load increased in the downstream direction and coincided with decreased in-stream nutrient removal, probably worsened by the significant chemical and geomorphological impairment found in the lower parts of the watershed.