The study aims at evaluating the quality of the water in the Ouémé River basin. Data were collected from October 2014 through September 2015. Physico-chemical parameters were assessed and the concentrations of dissolved heavy metals were determined. The results show both physical and chemical pollutions of the water according to a nonlinear pollution gradient. The middle basin up to the height of the city of Kaboua appears to be the most polluted segment. The Delta region, near the coast, is the second most polluted segment, and the remaining parts of the basin are the least polluted. Pollutant concentrations are highest during the low flow season. Cluster analysis and Principal Component Analysis (PCA) of sampled sites reveals that Atchakpa-Rejet and Kaboua have high concentrations of nitrite, nitrate, ammonium, orthophosphate, conductivity, TDS, pH, calcium, magnesium, and total hardness. Kpassa, Bétérou, and Atchakpa-Bethel have high dissolved oxygen and high transparency values. All other sites have high alkalinity. During the low flow season, Cd, Pb, Zn and Cu were detected at concentrations exceeding ecological standards in most of the sites. The Water Quality Index (WQI) ranged from 52.7 to 80.9, meaning that water in that river basin can be classified either as marginal quality, moderately polluted, or good quality for aquatic life. Overall, water in the Oueme River basin is under high and increasing influence of human activities.