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Sand barrier complex dynamics play a key role in defining coastal lagoon structure and functioning. Artificial manipulation of these dynamics for biased reasons (e.g., controlling floods, improving fisheries) aggravates conflicts between stakeholders and introduces potential threats to their conservation. This is the case at Laguna de Rocha, Uruguay, a protected area with international recognition, where the sand barrier opening has been the focus of a long-term conflict. A cooperative effort of scientists, authorities, and local stakeholders produced a breaching protocol, aimed to reduce conflicts while preserving the natural hydrodynamics of the system and its associated ecological processes. Historical information and present perceptions about the sand barrier breach were collected, and geomorphological and hydrological studies were carried out. Reconstruction of the historical management of the breaching practice showed that the artificial opening started in the 1950s and that the original procedure, performed by fishermen and cattle ranchers, was gradually left under to managers to, and it is presently performed with heavy machinery. Since the 1980s, inappropriate opening practices may have produced negative effects on the physical and biological structure of the lagoon. Geomorphological studies revealed the sand barrier as a highly vulnerable component of the lagoon and suggested that new opening sites could eventually develop over the long term, given the predictions of climate change and sea level rise. The hydrological approach provided an understanding of the processes driving the opening mechanism and the extent of the flooding of private and public lands. These results outlined the basis for the protocol, to support managers in deciding when to perform the opening, based on a reduced set of indicators (water depth, sand barrier berm elevation, and rainfall forecasts). Reaching a consensus was mainly based upon the existence, for more than 15 years, of a participatory advisory group discussing local environmental problems. The new sand barrier breaching protocol is a significant improvement over the previous situation, and can be generalized for application in similar contexts.