There is paucity of environmental data for Orani river systems in Bataan (Philippines) despite its regional economic and ecological significance. The present study conducted multivariate analyses of various water quality parameters and selected bacterial communities to evaluate the river’s health integrity. River data exhibited spatial and seasonal variation, with observed significantly distinct heterotrophic and Gram-negative bacterial counts in the midstream and downstream against upstream samples. Fecal coliform concentrations were statistically different in the sequence: upstream < downstream < midstream. Multivariate Principal Component Analysis identified the most important variables affecting the variability in bacterial concentrations among the sampling groups (81.64% variation). Cluster analysis also revealed the associations and similarities of sampling groups based on abundance of bacterial loadings. Further, water quality indices were classified within “marginal” class (54.77 for wet season; 57.67 for dry season). The hydrological index estimated a score of 47.97 for wet season that described as “suitable with high restriction” class (30<(HI)c<55), and 62.24 for dry season in the “suitable with medium restriction” class (55<(HI)c<75).