Even though the role of ecosystem services is known, the identification and assessment of water-related services is usually absent or often less represented as an ecosystem service. Progress in water quality indicator definition and compliance with regulations has been made; however, the relationship between water quality degradation and benefits to individuals and ecosystems remains little recognized. Here, we present an assessment of water quality and identification of ecosystem services in south-east Mexico. This study was performed within the geohydrological reserve zone of the Ring of Sinkholes, Yucatán Peninsula. Thirteen ecosystem services provided by the aquifer were identified. Water quality was evaluated in sinkholes based on national and international norms, considering different sinkhole uses. Results show a dynamic system, without saltwater intrusion and good to excellent water quality. The research demonstrates the relationship between ecosystem services and water quality, showing pressure in services related to uses for aquatic life protection and to a lesser extent those related to consumption. Current productive activities showed no pressure at this time. Principal Component Analysis (PCA) and Analysis of Variance (ANOVA) exhibited a significant difference in parameters and campaigns, but not between sinkholes. A long-lasting monitoring program for water quality is necessary to accurately evaluate the status of ecosystem services provided by the aquifer. Moreover, it is necessary to assess aquifers as ecosystems with economic, ecologic and socio-cultural importance. Effective water governance requires a balance of interests between all parties, within a legal and institutional framework.