Karst groundwater is the main source of water supply for ecosystems that are dependent on its discharges, such as wetlands, which are habitats for various species. Due to their characteristics and significance, it is imperative to conduct research aimed at elucidating the mechanisms governing the water quality and quantity in ecosystems reliant on karst groundwater discharges. The karstic systems are susceptible to contamination, and despite this fact, there is a dearth of information available, which hampers the accurate determination of water quality. The site study is the karst groundwater system discharging in the RAMSAR wetland Ciénaga de Tamasopo (Mexico) affected by the water extraction for the extensive sugar cane agriculture. The goal was to identify the groundwater flow systems discharging into the wetland by using hydrogeochemical and isotopic techniques. Additionally, it aimed to assess the temporal changes in physical and chemical parameters. It was determined that the chemical composition of the water changes with respect to residence time in the subsoil, and the predominant processes are the dissolution–precipitation of calcite, dolomite, and gypsum by water-rock interaction, mixing, and evaporation. This study facilitated the development of a conceptual model for understanding the movement of groundwater in karst systems in a warm, sub-humid climate. This conceptual model is crucial for enhancing water management strategies in the area.