Water agreements between Mexico and the United States have been crucial to preserving and restoring the Colorado River Delta's wetlands. Nowadays, increased water demand and climate change in the Colorado River Basin could threaten the conservation of the Ciénega de Santa Clara, a 4709 ha coastal wetland at the Sonoran Desert's edge. The international Ramsar convention recognizes the Ciénega de Santa Clara ecosystem for providing vital ecological services, including habitat for endemic, endangered, and migratory species. The hydrology of this wetland has not been completely understood since the 2010-2011 trial run of the Yuma Desalting Plant. Therefore, this study was conducted to identify and quantify the hydrological elements essential for the conservation of this wetland, under three scenarios: (a) normal inflow conditions of the water sourcethe Wellton-Mohawk canal; (b) inflow reductions, and; (c) an increase of temperature due to global warming. Water and mass balances estimates were conducted every month during 2014-2015; in situ measurements of inflows were carried out on Southern International Boundary in Wellton-Mohawk canal, the Riíto Drain, groundwater, and precipitation: evapotranspiration outputs were estimated using local weather stations and Penman-Monteith formulations. Temperature increases were based on the Intergovernmental Panel on Climate Change projections for the next 100 years. Results showed disconnection in the surface flow of water from the wetland to the adjacent Gulf of California. This behaviour was observed mainly in the summer months in the three scenarios. The disconnections reduced the wetland area and water storage. The hydrological functionality of the Ciénega de Santa Clara wetland depends on the water supply from the Wellton-Mohawk canal, with a minimum continuous discharge of 5.10 m 3 s −1 during the summer months.