Freshwater fish production is significantly correlated with water temperature, which is expected to increase under climate change. This study evaluated changes in water temperature and their impact on productive ponds at fisheries in the Czech Republic. A model was developed to calculate surface water temperature based on the five-day mean of the air temperature and was then tested in several ponds in three major Czech fish production areas. The output of the surface water temperature model was compared with independently measured data (r = 0.79–0.96), and the verified model was then applied to predict climate change conditions. The results were evaluated with regard to the thresholds characterizing the water temperature requirements of fish species and indicated that the limitation of Czech fish farming results from (i) an increased number of continuous periods during which given fish species are threatened by high water temperatures and (ii) the extension of continuous periods with stressful water temperatures. For Czech fisheries, the model suggests a sharp increase in unprecedented temperature regimes, which will pose critical challenges to traditional forms of common carp farming within several decades. Although reducing the level of eutrophication and loading them with organic substances might alleviate expected threads, farming current fish species in deeper and colder ponds at higher elevations might be inevitable.