Assessing Water and Sediment Contamination in the Sub-Middle São Francisco River (Brazil): Combining Physicochemical Analyses, Trace Metals, and Allium cepa L. Ecotoxicity

The Sub-middle São Francisco River (Northeast Brazil), a key water resource for regional socioeconomic development, is increasingly threatened by urban, industrial, and intensive irrigated agricultural activities. This study aimed to assess physicochemical parameters, nutrient and trace metal concentrations, and the phytotoxic, cytotoxic, and genotoxic effects of water and sediment samples collected from areas receiving urban–agricultural (A1, Juazeiro) and urban–industrial (A2, Petrolina) effluents during the dry and rainy seasons. Phosphorus and ammonia exceeded the limits established by CONAMA Resolution No. 357/2005 in Area 1 (A1). In water samples, Ni, Pb, Cu, and Fe exceeded regulatory limits in both areas, whereas Cr exceeded the sediment quality guideline only in A1 during the rainy season. Contamination levels were generally higher at effluent discharge points and varied seasonally. The Allium cepa bioassay revealed phytotoxic, cytotoxic, and genotoxic effects in both water and sediment samples, with genotoxicity representing the most sensitive biological endpoint. Correlation analyses showed no consistent associations between individual contaminants and biological endpoints after correction for multiple comparisons, suggesting that the observed biological effects were more likely related to the combined influence of multiple environmental stressors. These findings highlight the importance of integrating cytogenetic bioassays with physicochemical analyses to improve environmental quality assessment.