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This study assesses the spatial and temporal physico-chemical quality of the surface waters of Moulouya River based on the global pollution index PI. Several physico-chemical parameters (T°C, pH, electrical conductivity (EC), dissolved Oxygen (DO), BOD5, PO43−, NH4+, SO42− and NO3−) were monitored on 66 samples collected in 2014 during three campaigns at 22 stations from the upper reaches in the Upper Moulouya to its mouth in the Mediterranean. The results show that 86.4% of the stations show no pollution and are mainly located upstream of Moulouya river during the three campaigns of 2014 (March–April, May–June and July–August). However, the Zaida (M6), Missour (M12) and Gercif (M16) stations have polluted waters related to the very high levels of ammonium, nitrates, sulphates, phosphates and DBO5, which exceed Moroccan standards and would be related to the anthropogenic impact of agricultural fertilizers and urban and industrial wastes.