Groundwater Recharge (GR) is a crucial part of sustainability studies since it is one of the key factors responsible for making the groundwater resource renewable. An optimum strategy for responding to water level decline is artificial groundwater recharge. Artificial groundwater recharge projects are limited by cost, and the effective area is less. The role of natural factors for groundwater recharge is well defined and recognized in arid regions, whereas it’s challenging for humid areas. The current study’s main aim is to understand the contribution of the bio-geophysical aspect to groundwater recharge in the subtropical monsoon state of Uttar Pradesh in the Gangetic Plain. However, recharging is also one of the least understood processes because it changes over time and space and is challenging to quantify directly for a larger area. This research applied the ‘water and energy transfer among bare soil, vegetation, and atmosphere (WetSpass)’ model to estimate direct natural GR for Uttar Pradesh. The model’s output and its regression processes with climate, slope, soil type, and vegetation give a comprehensive understanding of natural controlling factors. Among the aforementioned controlling factors, though climate sharpens recharge dominantly, vegetation has shown a significant role in some areas of the state. In contrast to the prevailing view, vegetation cover can enhance groundwater recharge in the state. Thus, planting, and various tree management options, including groundwater-feeding species as a secondary plantation in cropland, can improve groundwater resources.