In this study, heavy metal pollution in Batlama stream flowing into the Black Sea from Giresun (Turkiye) province and the toxicity induced by this pollution were investigated by Allium test. Heavy metal concentrations in stream water were analyzed by using ICP-MS. Germination percentage, weight gain, root length, micronucleus (MN), mitotic index (MI), chromosomal abnormalities (CAs), proline, chlorophyll, malondialdehyde (MDA), antioxidant enzyme activities were used as indicators of physiological, cytogenetic and biochemical toxicity. In addition, Comet assay was performed for detecting DNA fragmentation. Anatomical changes caused by heavy metals in the root meristem cells were observed under the microscope. A. cepa bulbs are divided into two groups as control and treatment. The bulbs in the control group were germinated with tap water and the bulbs in the treatment group were germinated with stream water. As a result, heavy metals such as Al, Ti and Co and radioactive heavy metals such as Rb, Sr, Sb and Ba were detected in the stream water above the acceptable parametric values. Heavy metals in the water caused a decrease in germination, root elongation, weight gain, MI and chlorophyll values, and an increase in MDA, proline, SOD, CAT, MN and CAs values. Comet assays indicated the presence of severe DNA damage. In addition, heavy metals in stream water caused different types of CAs and anatomical damage in root meristem cells. As a result, it was determined that there is intense heavy metal pollution in the stream water and this pollution promotes multi-dimensional toxicity in A. cepa, which is an indicator organism. For this reason, the first priority should be to prevent pollution of water resources in order to prevent heavy metal-induced toxicity in water.