The Guarani Aquifer System (GAS) covers 1,088,000 km2, 68% of which is in Brazil, 21% in Argentina, 8% in Paraguay, and 3% in Uruguay. It is one of the most important aquifers on the continent and one of the largest transboundary aquifers in the world. More than 15 million people share this resource. Extensive analysis of existing documentation, supported by research questions, resulted in classification of five cooperation phases regarding management of the GAS: (i) 1970–2000, where scattered initiatives tried to grasp the aquifer’s geological and hydrogeological features as well as its regional circulation dynamics; (ii) 2000–2003, time needed for developing the project proposal; (iii) 2003–2010, the period marking the beginning of the official launching of the Environmental Protection and Sustainable Integrated Management of the Guarani Aquifer (GASP), funded by the Global Environmental Facility, the implementation of which lasted until 2009. This period was marked by intense cooperation efforts and concrete partnership achievements, including the Strategic Action Plan and, later, the Guarani Aquifer Agreement (GAA); (iv) 2010–2017, marked by a slowdown in transboundary cooperation, limited to sporadic cross-border projects, and some new local/national projects; and (v) 2017–present the benchmark of which is the ratification of the GAA by the four countries, a bright and formal move forward. Water availability in the region is extensive, and the absence of transboundary conflicts within the GAS has created a sense of abundance that is leading, unfortunately, to a lack of proactivity in terms of agreement implementation. The consequences are clear: data and tools developed by the GASP have not been updated; there has been a disruption of cooperation and administrative networks; there has been a loss of momentum generated by the GASP by societies and stakeholders; and there has been a loss of opportunities for detailed assessments to manage the aquifer’s heterogeneities and dynamics. Absent any coordinated approach, chances to obtain international funds are diminishing. There is no doubt that the GAA is one of the first examples of groundwater-related hydrodiplomacy—a negotiation process that seeks to simultaneously balance national interests and strengthen regional and local cooperative governance in aquifers shared between countries. Thus, the GAA should be considered a model, both for fulfilling requirements of international treaties and for designing an integrated water resource management approach.