The decreasing trend in rainfall in the last few decades over the Indo-Gangetic Plains of northern India as observed in ground-based observations puts increasing stress on groundwater because irrigation uses up to 70% of freshwater resources. In this work, we have analyzed the effects of extensive irrigation over the Gangetic Plains on the seasonal mean and intra-seasonal variability of the Indian summer monsoon, using a general circulation model and a very high-resolution soil moisture dataset created using extensive field observations in a state-of-the-art hydrological model. We find that the winter-time (November–March) irrigation has a positive feedback on the Indian summer monsoon through large scale circulation changes. These changes are analogous to a positive North Atlantic Oscillation (NAO) phase during winter months. The effects of the positive NAO phase persist from winter to spring through widespread changes in surface conditions over western and central Asia, which makes the pre-monsoon conditions suitable for a subsequent good monsoon over India. Winter-time irrigation also resulted in a reduction of low frequency intra-seasonal variability over the Indian region during the monsoon season. However, when irrigation is practiced throughout the year, a decrease in June–September precipitation over the Gangetic Plains, significant at 95% level, is noted as compared to the no-irrigation scenario. This decrease is attributed to the increase in local soil moisture due to irrigation, which results in a southward shift of the moisture convergence zone during the active phase of monsoon, decreasing its mean and intraseasonal variability. Interestingly, these changes show a remarkable similarity to the long-term trend in observed rainfall spatial pattern and low-frequency variability. Our results suggest that with a decline in the mean summer precipitation and stressed groundwater resources in the Gangetic Plains, the water crisis could exacerbate, with irrigation having a weakening effect on the regional monsoon.