Previous study of this research group revealed that water from the Billings reservoir (Brazil) intended for human use (water supply and seafood) has microbiological contamination and causes lethality and brain and behavioral impairments in zebrafish. The objective of this study was to understand what have induced these impairments in the animal model. Chemical analyses on water samples from Rio Pequeno (RP), Rio Grande (RG), and Bororé (BO) rivers, as well as chemical and morphological analyses on zebrafish gills exposed to those waters were performed. Waters samples from RP, RG, and BO presented high levels of phosphorus. BO water and fish gills exposed to this water presented high levels of nitrogen. RG water caused potassium contamination in gills. Phosphorus, nitrogen, and potassium are indicators of anthropogenic pollution. RG water and fish gills exposed to this water presented low levels of calcium, which might be an indication of chemical imbalance that could lead to health problems in aquatic animals. RG and BO waters resulted in zirconium contamination in gills. BO water induced respiratory lamellae thickening in the gills, which may be the underlying mechanism for the observed hypoxia. In conclusion, behavioral, brain, and respiratory defects observed previously were induced by chemical and morphologicalb disturbances due to anthropogenic pollution in the Billings reservoir.