Most studies on the effects of water quality on amphibians concern experimental conditions. The main aim of our study was to determine whether the quality of water bodies in urban environment may be a factor leading to local extinction of some amphibian species. We investigated the current amphibian richness in Kraków water bodies and the water quality of these water bodies. We compared our results with available historical data on amphibian richness in Kraków and we determined the number of amphibian species local extinction for each water body. Then, we compared water bodies with low amphibian extinction rates to water bodies with high amphibian extinction rates in respect to ten water quality chemical indicators. We found that the values of most chemical indicators were higher in water bodies with high amphibian extinction rates. The values of magnesium and chloride ion concentration, as well as conductivity appeared to differ the most between these two types of water bodies which is connected mainly with spring run-off into the water bodies. The results of this study demonstrate that water pollution may lead to local extinction of amphibian species.