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Water availability in arid regions is both sporadic and highly variable in quantity. If the water quality shows large variations of salinity and concentration of other chemical constituents with depth and time span, it has considerable effect on the entire hydrological set up of the area. In the Saidabad tahsil area, the deep aquifers that supply water to borewells in the alluvial plain of the Mathura region, Uttar Pradesh, have higher salinity than those of the dugwells from the shallow aquifers. The excessive drilling of tubewells and high yield tubewells are resulting in deterioration of water quality of the shallow aquifers. On the contrary, the chemical constituents such as, Na+, K+, Cl-, and HCO3- show higher concentration in shallow aquifers than deep aquifers. A study carried out to monitor water quality in this region reveals that the groundwater quality varies with depth and time span in shallow and deep aquifers. Factors controlling variations in salinity and concentration of chemical constituents of the water in the two types of aquifers are discussed. The relative merits of the shallow water for potability are pointed out with respect to salinity concentrations and public health.