Groundwater quality is a serious concern in alluvial aquifers undergoing vast agricultural transformation around the globe. Mehsana district of Gujarat is an example of agricultural landscape having most of the seasonal crops and vegetables. Groundwater samples were collected in monsoon 2017 and pre-monsoon 2018 to analyze major ions and isotopes to derive the hydrochemistry. The hydrochemical facies reveal Na+-Cl-, Na+-HCO3- and Ca2+-HCO3- type water suggesting complex hydrochemical reaction taking place in the region. The scatter plot of Ca2++Mg2+ versus HCO3-+SO42- and Na+ versus Cl- shows the ion exchange and silicate weathering along with intermixing of saline water. The presence of high sodium, alkaline pH and bicarbonate promotes the release of fluoride from minerals in groundwater which is high during monsoon. The fluoride concentration increases progressively along the Sabarmati River. The spatial variation map of nitrate in the district shows both point and non-point sources of NO3- contamination. This evidence will support the strong contribution of agricultural activities, as shown by land use that long-term flood irrigation practices have enhanced this impact. The deep aquifers are suitable for drinking purposes as compared to shallow aquifers which are affected with NO3- pollution due to the leaching process during the pre-monsoon season. The agriculture indices show contaminated groundwater for irrigation in more than 50% of wells. The composition of isotopes varied between (delta O-18 -2.08 to -4.41 parts per thousand and delta D -19.19 to -32.28 parts per thousand). The groundwater trendline was found below the local meteoric water line which indicates evaporation due to semiarid climate before infiltration.