End points of reproductive toxicity were investigated in male mice (Mus musculus, ICR) fed Nanjing City tap water for 90 days. There was no significant alteration in body weights between treatment and control mice. In treated mice, flow cytometry analysis of testicular tissue indicated that the relative percentage of the elongated spermatid (HC) decreased significantly (P < 0.05). Also slight increases in the relative percentage of round spermatids (1C) and primary spermatocytes (4C) were noted. The ratios of 4C:2C (diploid germ cells) and 1C:2C increased, and testicular histopathology indicated an expansion of interstitial space and a decreased number and size of Leydig cells in treated mice. The current study suggests that Nanjing City tap water is toxic to the reproductive system of mice and additional study to evaluate its effects on other species, including human beings, would be warranted.