Understanding groundwater systems is crucial to ensure their monitoring and protection. Global groundwater models and predictive tools exist to better understand them. In view of scarce groundwater data, especially in developing countries, the question of how to model these systems and make them usable for groundwater management is crucial. Herein, we demonstrate how a transdisciplinary process can overcome the data scarcity problem and lead to the development of a local groundwater balance model (LGBM). Over 50 actors from more than 15 disciplines and groundwater-related sectors were involved for the case of Yucatan, Mexico. Results revealed high wastewater emissions to the aquifer discharged without treatment and poor recycling practices. The method can be adapted to specific regions, can be used to address methodological challenges for monitoring, and can contribute to the achievement of the 2030 Development Agenda by addressing Sustainable Development Goal 6-related Targets (6.3, 6.4, 6.5, 6.6(a, b)).