This study was conducted to assess the relationship between environmental factors and the composition of fish assemblages from four interconnected rivers traversing several communities of Bayog Watershed comprising two provinces of Zamboanga in the Philippines. The distribution, abundance, and diversity of fish species in relation to the physicochemical parameters of the Sibugay, Dipili, Depore, and Guinoman rivers were obtained. A total of 1,004 fish individuals were collected during the field sampling and distributed into 11 families, 13 genera, and 18 species. The genus Oreochromis and Barbodes had the highest abundance and were prevalent in all the sites. Sibugay river obtained the highest Shannon-Weiner diversity index value (H’=2.05) and several species (14), while Guinoman has the lowest (species=11; H’=1.671). Sibugay river has the highest pH value (7.53), while Depore has the most deficient and acidic sites. Water temperatures were higher in Depore and significantly different from all other sites except in Guinoman. Influenced of environmental factors on the assemblages of freshwater fishes showed that depth (-0.894), pH (-0.813), and water temperature (0.859) were the three factors that are highly correlated with the first ordination axis in the CCA while dissolving oxygen (-0.250), and pH (-0.308) were positively associated with the second ordination axis. The biplot obtained from abundance and environmental data revealed that P. disjunctivus and T. trichopterus are positively associated with elevated water temperature and low pH. These introduced species can tolerate high temperatures and slightly acidic water. As observed in the study, channel water from the residential area, industrial waste, and effluents from agricultural activities are of most concern among the activities that affect the ecosystem.