Four thermal springs were sampled bimonthly for one year to determine their physicochemical and microbiological characteristics. Eleven physicochemical parameters, total coliforms, fecal coliforms and free-living amoeba were determined. In Mexico there is few works related with the quality of water from thermal springs, so this work helps to know the quality and some characteristics of this type of waters. The springs were classified by temperature as hypothermal and by the sulfates in the water as sulfate waters. From the dissolved salts content we determined that three were mineral waters and one was medium mineral water. The springs were hard water and carbonated or non-carbonated, predominantly the latter. Based on Ecological Water Quality Criteria, two springs exceed the recommended limit of 200 MPN/100 ml fecal coliforms in freshwater or seawater for recreational use with direct contact. Of the total, 83% of the samples tested positive for free-living amoebae and 7 genera were isolated; of these Naegleria was present in all the sampled sites. In general, the springs presented higher microbiological contamination in the pools than in the springs themselves due to the presence of bathers. The detection of total and fecal coliforms and the presence of thermophilic amoebae of the genera Acanthamoeba and Naegleria in the springs represent a health risk for users.