Chemical pollutants represent a leading problem for aquatic ecosystems, as they can induce genetic, biochemical, and physiological changes in the species of these ecosystems, thus compromising their adaptability and survival. The Capibaribe River runs through the state of Pernambuco, located in northeastern Brazil, and passes through areas of agricultural cultivation, densely populated cities, and industrial centers, primarily textiles. Despite its importance, few ecotoxicological studies have been conducted on its environment and knowledge about pollution patterns and their effects on its biota is scarce. The objective of this study was to evaluate the water quality and the damage caused by pollutants on the DNA specimens of Nile tilapia (Oreochromis niloticus) obtained from seven strategic points of Capibaribe. Tilapia specimens and water were collected during the rainy and dry seasons from 2015 to 2017. The following characteristics were analyzed: physicochemical (six), metal concentration (seven), local pluviosity, micronuclei and comet assay. The physicochemical and heavy metal analyses were exploratory, whereas the ecotoxicological analyses were hypothetical. To verify this hypothesis, we compared the groups of fish collected to the results of the micronuclei test and comet assay and created a Structural Equation Model (SEM) to determine how the micronuclei variables, damage index, pluviosity, and concentration of each metal were related. Our results demonstrated that the highest values for markers of genetic damage were detected at points with the highest heavy metal concentrations, especially iron, zinc, manganese, chromium, and cadmium. The SEM demonstrated that metals can explain the findings of the genotoxicity markers. Moreover, other pollutants, such as pesticides, should be considered, particularly in places where the river passes through rural areas. The results presented here demonstrate that the Capibaribe River has different degrees of contamination and confirm our hypothesis.