In many parts of the world, wastewater irrigation has become a common practice because of freshwater scarcity and to increase resource reuse efficiency. Wastewater irrigation has positive impacts on livelihoods and at the same time, it has adverse impacts related to environmental pollution. Hydrochemical processes and groundwater behaviour need to be analyzed for a thorough understanding of the geochemical evolution in the wastewater irrigated systems. The current study focuses on a micro-watershed in the peri-urban Hyderabad of India, where farmers practice intensive wastewater irrigation. To evaluate the major factors that control groundwater geochemical processes, we analyzed the chemical composition of the wastewater used for irrigation and groundwater samples on a monthly basis for one hydrological year. The groundwater samples were collected in three settings of the watershed: wastewater irrigated area, groundwater irrigated area and upstream peri-urban area. The collected groundwater and wastewater samples were analyzed for major anions, cations and nutrients. We systematically investigated the anthropogenic influences and hydrogeochemical processes such as cation exchange, precipitation and dissolution of minerals using saturated indices, and freshwater-wastewater mixtures at the aquifer interface. Saturation indices of halite, gypsum and fluorite are exhibiting mineral dissolution and calcite and dolomite display mineral precipitation. Overall, the results suggest that the groundwater geochemistry of the watershed is largely controlled by long-term wastewater irrigation, local rainfall patterns and water-rock interactions. The study results can provide the basis for local decision-makers to develop sustainable groundwater management strategies and to control the aquifer pollution influenced by wastewater irrigation.