In water ecosystems, many studies are being carried out in order to identify the damage caused by polluting parameters. Because of the insufficient wastewater treatment, Izmit Bay is getting polluted. Thus, it is aimed to investigate the phytotoxic and genotoxic effects of water samples taken from Eastern Channel of Kocaeli on some plants with economic value. The seeds of Vicia faba and Zea mays were treated with 3 different concentrations of water samples (40, 80, 100%), and control groups were germinated in distilled water. The phytotoxic effects were determined by morphological and anatomical experiments, whereas genotoxic effects were determined by cytological experiments. Leaf anatomy, seed germination percentages, mitotic index, mitotic abnormalities, chlorophyll and carotenoid contents were determined. Several deformations were observed in leaves of treated plants. Root lengths were increased in treated groups of V. faba, and decreased in treated groups of Z. mays. All the concentrations used caused several abnormalities in mitotic cell divisions and decreased the mitotic frequency in the root tip cells. Micronucleus, chromosomal bridges, laggard chromosome, polar slip and lack of cytokinesis, and some other abnormalities were observed in different phases of mitosis.