The study investigates the spatial and temporal variation in water quality parameters at nine different locations in Mé, Bété and Djibi Rivers as well as Aghien Lagoon near Abidjan city for twelve consecutive months. Physicochemical parameters concerned are pH, temperature, electrical conductivity, dissolved oxygen, chlorophyll-a, total phosphorus and total nitrogen. Dissolved heavy metals analyzed are Ni, Cu, Zn, Pb, Cd and As. The assessment of physicochemical parameters shown the deteriorate of water quality with significant changes particularly in the Djibi River with high mean concentrations of total phosphorus (0.51 mgP.L-1) and total nitrogen (7.60 mgN.L-1). Nevertheless, the overall mean concentrations of heavy metals in water Cu (1.43 µg.L-1), Cd (0.06 µg.L-1), Pb (0.2 µg.L-1), Zn (9.16 µg.L-1), As (0.3 µg.L-1), Ni (2.77 µg.L-1) were lower than WHO Standard for Drinking Water Quality. Dissolved heavy metal percentage indicates that the order of concentrations was Zn>Ni>Cu>Pb>As>Cd. Multivariate analysis of variance (ANOVA) was used to group the different sampling sites on the basis of spatial similarities and classification, based on contamination sources and origin of pollutants in rivers and lagoon. In conclusion, this study clearly infers the fact that the cause of pollution in this region is mainly due to domestic and industrial effluents, agriculture and finally natural source.