Watershed management requires information that allows the intervention of possible sources that affect aquatic systems. Surface water quality in the Cunas river basin (Peru) was evaluated using multivariate statistical methods and the CCME-WQI water quality index. Twenty-seven sampling sites were established in the Cunas River and nine sites in the tributary river. Water samples were collected in two contrasting climatic seasons and the CCME-WQI was determined based on physicochemical and bacteriological parameters. The PCA generated three PC with a cumulative explained variation of 78.28 %. The generalised linear model showed strong significant positive relationships (p < 0.001) of E. coli with Fe, nitrate, Cu and TDS, and a strong significant negative relationship (p < 0.001) with pH. Overall, the CCME-WQI showed the water bodies in the upper reaches of the Cunas River as good water quality (87.07), in the middle reaches as favourable water quality (67.65) and in the lower reaches as poor water quality (34.86). In the tributary, the CCME-WQI showed the water bodies as having good water quality (82.34).