In arid and semiarid zones, groundwater plays a key role in the ecology and availability of freshwater. Coastal lagoons in arid zones have great importance as a refuge for species of flora and fauna, as a source of freshwater, and for recreational purposes for local communities and tourism. In addition, as environments under natural stress, they are suffering pressure from anthropogenic activities and climate change, especially in zones with intense touristic development as in the case of the Baja California Peninsula in northwest Mexico. In this paper, we analyze the future of a coastal lagoon impacted by climate change and anthropogenic pressures. We constructed a groundwater MODFLOW-SWI2 model to predict changes in freshwater–saltwater inputs and correlated them with the geospatial analysis of the distribution and evolution of the water body and surrounding vegetation. The methodology was applied to the San Jose lagoon, one of the most important wetlands in the Baja California peninsula, which had been affected by anthropogenic activities and endangered by climate change. According to our water balance, the deficit of the San Jose aquifer will increase by 2040 as a result of climate change. The water table north of the lagoon will drop, affecting the amount of freshwater inflow. This reduction, together with an increase of evapotranspiration and the sea-level rise, will favor an increase of mineralization, reducing the surface water and groundwater quality and in consequence affecting the vegetation cover. Without proper management and adequate measures to mitigate these impacts, the lagoon may disappear as a freshwater ecosystem. Results of this research indicate that the use of a groundwater flow model, together with a geospatial analysis provide effective tools to predict scenarios for the future of coastal lagoons, and serve as a basis for land planning, nature conservation, and sustainable management of these ecosystems.
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