Anthropogenic pollution significantly contributes to the global decline in surface water quality, particularly in India where the lack of adequate test facilities and testing capacity severely limits water quality monitoring. In this study, we investigated eight surface aquifers of Dehradun—capital city of Uttarakhand, India and analysed them using the water quality index—WQI and to evaluate the influence of urbanization on the surface water characteristics by employing the weighted arithmetic quality index method. The quality of the water was assessed by data set of 14 physico-chemical and microbiological parameters. The WQI of the sampling locations varies from 42.057 to 50.159 (good—poor quality) during monsoon season and ranged from 60.136 to 98.592 (poor—very poor) during the pre-monsoon tenure. Among surface aquifers analysed, 56% samples were in the “poor” to “very poor” status during both seasons. Further, Most Probable Number (MPN) values (Coliform bacterial analysis) were exceeded the tolerable limits at all the sampling sites. The Sustainable Development Goals—SDG 6 targets to coordinate global efforts for “clean water and sanitation.“ However, the SDG target of clean water in the lives of people around the world cannot be accomplished if the water is contaminated with pathogenic bacteria or faecal coliforms. It was observed from study that the river segments within the urban core are primarily deteriorated due to illegal discharge of sewage, increased urbanization, unprotected river sites, slum areas, lack of proper sanitation, anthropogenic activities and urban runoff. Urban authorities must take cognizance of the same to ensure the smart city project accomplishment in Dehradun.