This paper presents the results of the variability of the water pollution index (WPI) and water quality index (WQI) in the Manzanares River basin, located in northeastern Venezuela, in relation to climatological conditions during the period 2005–2022. The variables involved were measured at fifteen stations distributed throughout the river system during six sampling periods. A principal component analysis (PCA) was performed to validate the variability of the applied indices, and a cluster analysis was conducted to identify similarities among the stations. The water quality estimation using the WQI model showed that the Manzanares River basin exhibited values meeting criteria for medium quality in the upper basin; medium to poor quality in the middle basin; and poor quality in the lower basin. The ICO also reflected contamination by nutrients, suspended solids, mineralization, and organic matter throughout the watershed, but with greater emphasis on the lower sub-basin, which was considered contaminated throughout the rainy season, as well as contaminated and highly contaminated during the dry season, according to the categorization of Ram írez et al. (1997). It was also observed that the concentrations of some pollutants decrease during the rainy season; however, during the dry season, the levels of contamination present in the river increase, indicating the persistence of pollution in this water body. Continued environmental monitoring and control of human activities are recommended.