The Massa basin in Morocco suffers from water scarcity and water quality degradation largely due to salinity and nitrate contamination. In this study, a multi-tracer approach, was used that integrated water chemistry, stable isotopes of water (18O, 2H) and stable isotopes of nitrate (15N, 18O), to investigate mineralisation and nitrate contamination in the Massa catchment. The main objective was to identify, for the first time in the area, water pollution sources, with an emphasis on nitrate-originated contamination using the 15N isotope. Water samples were collected from rivers, dams, wells, boreholes and springs, from different parts of the area (irrigated farms, along Massa River, Anti-Atlas Mountains and coastal areas). The results show a large variability of water mineralisation in space indicating rock-water interaction, sea-water intrusion and anthropogenic influence. The lowest mineralization value is measured in spring water located in the Anti-Atlas Mountains while the highest one is measured in Massa River. The results also show a large variability of NO3 with high contents in many sites. Some domestic wells showed the highest NO3 concentrations. The field investigation reveals a practise where domestic wastewater is being poured directly into traditional septic tanks. 15N results indicate mixing origins of nitrate related to sea-water intrusion, NH4 fertilizers and manure septic which constitute the main issue. Our results will be an essential recommendation for decision-makers for the implementation of wastewater treatment systems before they are discharged into the environment. Improving individual septic systems is also a necessary condition.