The goal of this work was to evaluate of water quality in natural swimming pools in Borovany and Sezimovo Ústí, to compare the differences in the results of water analyses in proper swimming water body and regenerative part, as well as to compare of both these localities. Most of results were gathered during 2016 in Borovany and during 2017 in Sezimovo Usti. Transparency, color of water, temperature, conductivity, concentration of dissolved O2, concentrations of NH4-N, NO2-N, NO3-N, TN, PO4-P, TP, Cl, turbidity, fluorescence, chlorophyll concentration, alkalinity, zooplankton and phytoplankton composition and bacterial contamination were monitored. The results confirmed the possibility to achieve the good water quality even though the problem with phosphorus removing remains. The comparison of both site showed more efficient functioning of regenerative zone in Borovany natural swimming pool.