This paper describes the prevalence of indicator and pathogenic bacterial groups in water and sediments in OSZ-offshore, ISZ-inshore, IEZ-inner estuary, and UEZ-upper estuary along the river Chapora, central west coast of India, which is influenced by anthropogenic inputs. The abundance of indicator bacterial groups such as total coliforms and Escherichia coli-like organisms in water ranged from non-detectable (ND) to 10 colony-forming units (CFU)/mL. In contrast, their abundance in the sediments was six orders magnitude higher than water (ND to 10 CFU/g). The abundance of potential pathogenic bacteria in water and sediment samples ranged from ND to 10 CFU/mL and from ND to 10 CFU/g respectively, with Shigella-like organisms (SHLO) being the most abundant. In the surface waters, SHLO and Pseudomonas aeruginosa-like organisms (PALO) and in bottom waters, Vibrio parahaemolyticus-like organism and PALO increased progressively from OSZ to UEZ. In contrast, Proteus/Klebsiella-like organisms (PKLO) showed a reverse trend. Amongst all four zones, IEZ was the most contaminated in terms of the higher abundance of indicator and potential pathogenic bacterial populations as corroborated by significantly lower water quality index value. Principal component analysis performed using physico-chemical variables and bacterial groups to reduce data set variability revealed that a different set of parameters contributed differently to the total variation in each zone. Considering the eco-sensitivity of the river Chapora, the results of the present study call for precautionary measures to minimize the degree of anthropogenic inputs.