The protection of the aquatic environment while managing the risk of water scarcity in the Mediterranean region is challenging. Ensuring future sustainability of water resources needs improved monitoring networks and early warning system of future trends of water quality. A specific concern is given to nonpoint source pollution from agriculture, which is often the main source of water quality degradation in rivers. In this work, we focused on the Joumine river basin, a rural-catchment situated north Tunisia dominated by agricultural activities and exposed to eutrophication problems. Aiming to present an assessment framework of the spatial-temporal water quality variability and quantify pressure-impact relationships, we used a physically based modeling approach involving the river/basin integrated model PEGASE (Planification Et Gestion de l'ASsainissement des Eaux). PEGASE simulates watercourses physicochemical quality depending on the morphology of the drainage network, hydrometeorological conditions and natural and anthropogenic influences. Simulation results showed a better description of Joumine river water quality and helped in identifying exposed areas to nutrients export. Results have also emphasized the contribution of different pollution sources. We were able to examine the potential impact of agriculture diffuse pollution and we found that Nitrate is the element mostly threatening water quality. The nutrients patterns suggest that climate and farming practices are important factors controlling their transfer. These findings demonstrate that the adopted assessment approach in investigating the behavior of the studied hydrosystem can be a useful support to develop an appropriate surface water quality management program in a semiarid context.