In order to understand the hydrogeochemistry of Mathura city, western Uttar Pradesh a total of 92, 34 and 22 groundwater samples were collected from shallow, intermediate and deep wells during post-monsoon 2017 and pre-monsoon 2018 respectively and analyzed for major cations and anions. The groundwater of the study area is found to be alkaline in nature and is categorized as hard to very hard water type. Dominant facies deciphered from Piper’s trilinear diagram of shallow, intermediate wells are Na-K-Cl-SO4 and Ca-Mg-Cl-SO4 while deep well samples are Ca-Mg-Cl-SO4 type facies in post-monsoon 2017. During pre-monsoon 2018, the ionic facies for shallow, intermediate and deep well samples is Na-K-Cl-SO4 type with the exception of 7 samples of shallow well which shows Ca-Mg-Cl-SO4 type facies. Based on the water quality index (WQI) classification, majority of samples of shallow, intermediate and deep well fall in poor water category in both seasons. According to pollution index of groundwater (PIG) classification, majority of samples of all three depths showed low to moderate pollution in both the seasons. Saturation indices of minerals was also calculated by employing geochemical program PHREEQC. Groundwater at shallow depth possesses excess concentration of Ca, Na, K, and SO4, followed by intermediate and deeper depth samples of both seasons. Trace elements like As, Mo, Sr, and Zn show higher concentration in shallow depth samples followed by intermediate and deeper depth samples, except As which shows a reverse trend. This demonstrates that the groundwater from shallow wells is definitely more vulnerable to contamination. The study has revealed poor groundwater quality of Mathura city and noticeable influence of urbanization and industrialization on water quality.