Human activities associated with intensive irrigation, reservoir storage, and groundwater pumping have substantially altered the hydrological cycle, environment, and regional climate in India. However, the role of human activities on water budget and droughts remains mostly unexplored. We use calibrated and evaluated Community Water Model (CWatM) to quantify the influence of human activities on agricultural (estimated using soil moisture) and hydrological (estimated using total runoff) droughts in India during 1951–2016. The simulations using the CWatM were conducted for the Natural (without human influence) and Human (with the human influence of irrigation, reservoir storage, and groundwater pumping) scenarios. Evapotranspiration and soil moisture increase while total runoff and groundwater storage decrease under the Human scenario in comparison to the Natural scenario. The dominant influence of human activities on agricultural and hydrological droughts was found during the monsoon and post-monsoon seasons. We find a contrasting effect of human activities on agricultural and hydrological droughts. While human activities reduced the intensity of agricultural droughts, hydrological droughts are intensified under the Human scenario. The intensification of hydrological droughts is linked to excessive water abstraction for irrigation. On the other hand, irrigation increases soil moisture and decreases the intensity of agricultural droughts. Overall, our findings highlight that excessive groundwater pumping and irrigation can intensify hydrological droughts, which can have considerable environmental implications.