The Hueco Bolson aquifer is a binational aquifer shared by the United States of America (USA) and Mexico that is strongly interconnected with the transboundary river, Rio Grande/Rio Bravo. Limited recharge, increasing urbanization, and intensified agriculture have resulted in the over-drafting of groundwater resources and stressed the aquifer, threatening its sustainability if mitigation actions are not taken soon. Research indicates that the aquifers hydraulic gradients and flow directions have changed due to the high groundwater withdrawal rates from the two major citiesEl Paso (USA) and Ciudad Juarez (Mexico). This paper presents a comprehensive overview of the Hueco Bolson aquifer modeling history and makes a case for future modeling and binational engagement efforts. First, we discuss the evolution of groundwater modeling for Hueco Bolson from the past to recent times. Second, we discuss the main water management issues in the area, including water quality and quantity, stakeholders participation, and climate change. To address the challenges of holistic water management, we propose developing a graphical quantitative modeling framework (e.g., system model and Bayesian belief network) to include experts opinions and enhance stakeholders participation in the model. Though the insights are based on a case study of Hueco Bolson, the approaches discussed in this study can provide new strategies to overcome the challenges of managing a transboundary aquifer.