The Tubarão River rises in Santa Catarina, Brazil, and has been historically affected by coal mining activities around its springhead. To evaluate its water conditions, an investigation regarding a possible decontamination gradient associated with the increased river flow toward the estuary, as well as the influence of seasonality over this gradient was performed through a series of biomarkers (vitellogenin, comet assay, lipid peroxidation, protein carbonylation, gluthatione, gluthatione S-transferase, acetylcholinesterase, light microscopy in liver, and scanning electron microscopy in gills) and chemical analysis (polycyclic aromatic hydrocarbons (PAHs) in bile and metal analysis in sediment) in the cichlid Geophagus brasiliensis. Two collections (summer and winter) were made in four distinct sites along the river, while sediments were sampled between those seasons. As expected, the contamination linked exclusively to mining activities was not observed, possibly due to punctual inputs of contaminants. The decontamination gradient was not observed, although seasonality seemed to have a critical role in the responses of biomarkers and availability of contaminants. In the summer, the fish presented higher histopathological damages and lower concentrations of PAHs, while in the winter they showed both higher genetic damage and accumulation of PAHs. The Tubarão suffers impacts from diverse activities, representing health risks for wild and human populations.