Introduction. In most thermal waters, the sanitary and microbiological quality is unknown, enabling the growth of certain microorganisms inherent to these environments, which have evolved to adapt to the extreme conditions of these ecosystems. The water quality depends on its physicochemical properties, such as temperature, pH, and electrical conductivity. Objective. To analyze the physicochemical and bacteriological status of the most visited thermal pools in Baños parish, Cuenca - Ecuador. Methodology. The study was descriptive, experimental, and cross-sectional. The universe was the three spas, "El Riñón" Spa, "Durán Inn," and “Durán" Spa, along with one spring sample, from where 16 samples were obtained for the physicochemical and bacteriological analysis of these spas. Results. In the bacteriological analysis, Staphylococcus aureus was identified with a percentage of 77%. In the physicochemical analysis, an average pH value of 7.92 was observed at "Riñón” Spa and in the spring, an average of 8.43 at "Durán Inn" and "Durán" Spa. The temperature was around 35 °C, except for the spring. Conclusion. These thermal waters depend on the physicochemical conditions; they are mesothermal and alkaline waters, and their microbiological quality is excellent since the presence of Staphylococcus aureus does not represent a risk for individuals who visit these recreational facilities.