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The groundwater salinity of Mendha river, one of the important streams that feed Sambhar playa in Rajasthan in western India, was studied to understand the effect of neotectonic activity on groundwater quality and salinity. We attempted to decouple the tectonic control of salinity and its contribution in the development of playa deposits in Rajasthan. Multiresolution, multidate satellite data products such as IRS-1C, IRS-1D LISS-III, PAN and Landsat MSS were digitally enhanced and analysed to model the morphotectonic evolution and hydrological regime of the region. Electrical conductance data from spatially distributed points in the Mendha river basin were correlated with the aquifer geometry deciphered from borehole lithologs and lineaments and major geomorphic features interpreted from satellite images. The results of the study reveal that the aquifer geometry is controlled by subsurface structures that have been influenced by neotectonic activity in the past 8-9ka, significantly influencing the hydrological regime and salinity of Sambhar playa.