Water pollution is a global environmental issue, and aquatic sediments are important compartments that might act as sinks or sources of contaminants. Once in the environment, inorganic contaminants such as metals can cause cytogenotoxic effects that damage genetic material and harm the aquatic community. Biological assays such as the Allium test can be used to investigate potential cytogenotoxicity of contaminated sediments based on the alterations of cell cycle indexes and chromosomal aberration frequencies. Therefore, we aimed to assess the toxicity of sediments from four Brazilian reservoirs using the Allium test. Sediments were sampled and elutriates were prepared in a simulating sediment resuspension in the water column. The Allium test was applied to the elutriates, and the metals copper, chromium, cadmium, lead, zinc, and iron were quantified. The elutriates derived from reservoir sediments were able to reduce the mitotic and anaphase index, increase the prophase and metaphase index, and boost chromosomal aberrations compared to the negative control. The cytogenotoxic effects observed may be linked to the presence of copper, zinc, and iron. Therefore, our results showed that the Allium test was a sensitive tool for warning the occurrence of genotoxic contaminants in sediment elutriates from four Brazilian reservoirs.