Thermal springs are important for community health since they are public places and being widespreadly used. Free-living amoeba are common in nature. Naegleria and Acanthamoeba species in particular are found in thermal springs and may cause serious health problems. At the first stage of the study, it is aimed to research the presence of Naegleria and Acanthamoeba species in thermal springs in Turkey while the second stage looks into the frequency of subtypes of these species by genotyping through molecular techniques. The results of the first stage are presented in this article. The second stage is currently in progress. This is the first research where all the thermal springs licensed in Turkey are included. The parasitological examination of 434 samples revealed that 34.1% of the samples were amoeba positive. Upon the completion of this study, the frequency of pathogen species and health risks linked to the amoeba will have been laid bare. Chlorination, FLA determination and typology should be incorporated into monitoring criteria for thermal spring water. To prevent health risks regarding amoeba, it would be beneficial to raise the awareness of users about hygienic practices and thwart health risks induced by amoeba in thermal springs.