The tap water must be disinfected in order to get rid of the disease-causing microorganisms. Most of the disinfection methods used in water treatment are decoction, chlorination, disinfection with ozone, disinfection with ultraviolet, disinfection with peracetic acid. The effects of sodium hypochlorite, calcium hypochlorite and peracetic acid was investigated on barley (Hordeum vulgare) and red worm (Eisenia fetida). The EC50 values for H. vulgare and LC50 values for E.fetida was determined by using these three disinfectants. Within three days of application, EC50 values for H.vulgare were found as 20 µl/ml for NaOCl, 240 mg/ml for Ca(ClO)2 and 80 µl/ml for PAA. At the end of 24 hours of application, LC50 values for E. fetida were 30µl/ml for NaOCl, 8mg/ml for Ca(ClO)2 and 25µl/ml for PAA. Cytotoxic effects were examined by the mitotic index and chromosomal abnormality test in H. vulgare. When compared with the control group, it was determined that increasing concentrations of NaOCl, Ca(ClO)2 and PAA decreased the mitotic index and caused chromosomal abnormalities in mitotic divisions on the root meristematic cells of H.vulgare. Alkaline single cell gel electrophoresis method was used to determine the genotoxicity of NaOCl and Ca(ClO)2 applications on E.fetida. Compared to the control group, it was determined that the degree of DNA damage after Ca(ClO)2 application was higher than NaOCl. Since these chemicals are able to create cytotoxic effects, they should also be used with caution at low concentrations.