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The freshwater-saltwater interface position in groundwater at coastal aquifers is determined by the location of the coastline. Anthropogenic-driven changes as modification of the land uses in catchments or the engineering construction in rivers can alter the transport of sediments to the coastal areas affecting to the coastline shape in detrital systems. This is the case of the Motril-Salobrena aquifer where the rapid coastline progradation over the last 500years generated new land previously covered by the sea at a fast rate, 3myear(-1) during hundreds of years. The effect of these changes in the salinity of the aquifer and the flushing time by freshwater has been examined with a paleo-hydrogeological model simulating the transient evolution of the groundwater salinity for the last 500years with SEAWAT. The results of the model indicate a differentiated flushing time depending on the hydraulic properties in the region ranging from 50years in the western sector to up to more than 200years in the central sector for the shallower parts of the aquifer. In the deeper layers, the time can be highly increased but the uncertainties in the hydraulic properties generate different scenarios both in flushing time and water circulation in the aquifer. The sectors in the aquifer where changes took place at a faster rate are also the most sensitive to the effect of global changes, especially those associated to human activity as they occurat shorter time periods.