The aim of this study was to (i) evaluate water quality using limnological parameters in three streams belonging to the Ivinhema River basin, (ii) investigate the composition and structure of the landscape around the locations sampled and their possible contribution to changes in water quality, (iii) investigate genotoxicity in fish in situ as environmental bioindicators, and (iv) evaluate the cytotoxic and genotoxic potential of water through bioassays in animal and plant models. A total of seven fish species were sampled in situ as bioindicators of environmental toxicogenetic damage: Astyanax fasciatus, Astyanax lacustris, Cyphocharax modestus, Moenkhausia forestii, Piabina argentea, Psellogrammus kennedyi, and Hypostomus ancistroides. Four types of nuclear and one cytoplasmic alteration were observed, with nuclear invagination being the most frequent. Animal bioassays showed five types of nuclear and one cytoplasmic alteration. In the plant bioassay, a reduction in germination and cell division was observed, indicating the cytotoxic and genotoxic effects of the water for Allium cepa cells. Thus, genotoxic alterations in fish and plant bioassays may reflect the different types of land use and cover around streams and the conversion of forest fragments into agricultural areas, mainly due to the expansion of sugarcane crops. The evaluation of the toxicogenetic status of the three streams is essential to emphasize the need to create projects to recover the native vegetation cover, which would improve the quality of the habitat and ensure the permanence of native species.