Low pressure ultraviolet photolysis proved to be an efficient treatment to achieve inactivation of different yeast species (Candida sp., Cryptococcus carnescens, Metschnikowia viticola/Candida kofuensis, Rhodosporidium babjevae, Rhodotorula minuta, and Rhodotorula mucilaginosa) isolated from water sources with very different compositions. The sensitivity degree of various yeast isolates to UV treatment varied among different genera. Species isolated from surface water gained additional photoprotective resistance as a defence mechanism to be able to survive under constant sunlight conditions compared to the groundwater isolates. Yeasts were found to be more resistant to UV treatment than E. coli, Cryptosporidium, and Giardia.