Groundwater is rapidly depleting in India primarily because of pumping for irrigation. However, the crucial role of crop growth at annual and seasonal timescales in groundwater storage variability remains mostly unexplored. Using the data from the Gravity Recovery Climate Experiment (GRACE) satellites and well observations, we show that crop growth is negatively correlated with groundwater storage at annual and seasonal time scales in north India. Precipitation is positively associated with groundwater storage variability at yearly time scale in the northcentral (NCI) and South India (SI). In contrast, precipitation is negatively correlated with groundwater storage from the GRACE satellites in northwest India (NWI). The negative correlation between precipitation and groundwater from the GRACE in NWI is primarily due to groundwater depletion due to anthropogenic pumping from deep aquifers. Precipitation and groundwater storage from the well observations are positively correlated in all the three regions indicating the influence of precipitation on shallow aquifers. Analysis of the two main crop growing seasons (Rabi and Kharif) showed that crop growth is negatively related to groundwater storage in both Kharif (June-September) and Rabi seasons in north India (NWI and NCI). Groundwater contributes more than precipitation in NCI during the Kharif season and in NWI and SI during the Rabi season. Granger’s causality test showed that groundwater is a significant contributor to crop growth in NWI and NCI in both Kharif and Rabi seasons. Our results highlight the need for agricultural water management in both the crop growing seasons in north India for reducing the rapid groundwater depletion.