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The Itapemirim River is considered one of the most important water resources in the state of Espírito Santo, Brazil. However, environmental problems due to continuous anthropogenic contamination are threatening its potential use. This study assessed water quality by analyzing abiotic and toxicogenetic aspects of the water from four stations along the river. Samples were collected in both dry and rainy seasons. Most of the abiotic variables were below the threshold established by CONAMA Resolution No. 357/2005, and so were most of the metals. However, Al and Cu contents were above those allowed by legislation, ranging from 0.2 to 0.9 mg/L. Regarding toxicogenetic aspects, genotoxic effects were observed in meristematic cells of Allium cepa, in micronucleus test and comet assay of Oreochromis niloticus, and CHO-K1 cells. Mutagenic effects were significant at RI 02 (0.34), RI 03 (0.46), and RI 04 (0.12) stations on the first campaign in A. cepa F1 cells, compared to the negative control (0.0). The second campaign revealed the same results, but with the addition of samples from RI 01 (0.17) and RI 03 (0.18) showing mutagenicity in the micronucleus test with fish erythrocytes when compared to the negative control (0.3). Essentially, all the samples evaluated in both campaigns showed damage in A. cepa, O. niloticus, and CHO-K1 cells, thus demonstrating that the water quality of the Itapemirim River is compromised and requires action plans for its recovery.