Disinfection of surface drinking water, in particular water chlorination, produces many by-products with genotoxic and/or carcinogenic activity. The aim of this research was to evaluate the genotoxicity of surface water after treatment with different disinfectants by means of in situ plant genotoxicity assays. The study was carried out in a pilot plant using lake water after sedimentation and filtration, which supplied four stainless steel basins: three basins were disinfected with sodium hypochlorite, chlorine dioxide and peracetic acid, respectively, and the fourth basin contained untreated lake water and was used as a control. The study was carried out using water collected in different seasons over a period of about one year in order to assess the treatments under different physical and chemical lake water conditions. Plant genotoxicity tests were performed by exposing plant bioindicators directly to raw and disinfected water. The Tradescantia micronucleus test in pollen cells of the flowers of an hybrid of Tradescantia and the Allium cepa test, a chromosome aberration test in root cells of Allium cepa, showed genotoxic effects only in some disinfected samples and revealed genotoxicity also in raw water in one experiment. The Vicia faba test, a micronucleus test in root cells of Vicia faba, revealed genotoxicity in many samples of disinfected water. The results of the study indicated that the Vicia faba/MCN test was the most sensitive plant assay for disinfected water, and that peracetic acid disinfection produced lower genotoxicity than sodium hypochlorite or chlorine dioxide treatment.