From collection to discharge: physical, chemical, and biological analyses for fish farm water quality monitoring. The use of chemical substances for the management of fish farming activities may compromise the quality of the tank water itself and of water bodies that receive the effluents. As studies that assess the environmental effect caused by pisciculture are scarce, the present study aimed at evaluating the water quality in two fish farms in the region of Grande Dourados, Brazil, from the site of water collection to the site of water disposal. The tools used for this purpose were the analysis of land use and cover and the determination of physical, chemical, and biological parameters of water samples. Maps of land use and cover were created, and water samples were collected at four sampling sites in two fish farms. The Allium cepa test, assays with Astyanax lacustris, and the Salmonella/microsome assay were performed. In addition, physical and chemical parameters were measured and metal and emerging contaminants in the water samples were investigated. The A. lacustris demonstrated the genotoxicity and the Salmonella/microsome assay suggested the mutagenic potential of water samples from the fish farms and indicated higher genotoxicity in the disposal tanks than in the collection tanks of the Brilhante fish farm. However, all the samples at the Dourados fish farm were genotoxic, and mutagenicity was shown to start at the water collection site. With regard to the A. cepa test, there was no statistical difference between the collection sites in both fish farms. Moreover, the observed genetic damage may be associated with the presence of metals and emerging contaminants in the water samples, which suggests that these chemicals have potential genotoxic and mutagenic effects that are related to the type of land use and cover in the area of the region studied. Considering that contaminated waters can potentially disturb the structure and functioning of natural ecosystems, the present study demonstrated the importance of treating fish farm effluent to minimize the negative effect of this activity on water bodies.