Sodium metabisulfite is used in marine shrimp harvesting to prevent the occurrence of black spots. Shrimps are soaked in a sodium metabisulfite solution in ice, which is disposed of in sewages that run into marine canals, creating an environmental hazard. This study evaluates the toxicity and mutagenicity caused by sodium metabisulfite in sea waters and sediments collected in a shrimp farm in Cajueiro da Praia (Luis Correia), state of Piauí, Brazil, using the Allium cepa assay. Water and sediment samples were collected in the dry and in the rainy seasons, in three sites: upstream the shrimp farm (Site 1), at the point sodium metabisulfite is discharged (Site 2), and 100 m downstream the farm (Site 3). Three sample dilutions were used (50%, 25% and 10%) for all samples. A negative control (well water) and a positive control (copper sulfate 0.0006 mg mL⁻¹) were used in each experiment. At the end of the 72-h exposure period, onion roots were measured and removed. Mutagenicity analysis included the determination of mitotic index, chromosomal aberrations and the detection of micronuclei; analysis of root size and mitotic index were used as an index of toxicity. The A. cepa assay revealed that the water and sediments samples collected in the Piauí coast contaminated with sodium metabisulfite induce toxicity. The results demonstrate that the assay may be used as a regular tool in the analysis of water parameters in shrimp farms in the coast of Piauí state, and in strategies to preserve the region's marine ecosystem.