Groundwater based irrigation is one of the key factors for rapid agricultural development in India. Therefore, understanding the sustainability of irrigation water management is utmost important for agriculture. This study investigated the sustainability of groundwater based irrigation by identifying recent (1996–2017) trend in groundwater depth using Mann-Kendall (MK) test or Modified MK and Sen's slope analysis. This study also explored the relationships of groundwater depth with rainfall and irrigated areas in lower Ganga River basin in India with an area 195,601 km2. Results showed that almost 81.78%, 66.22%, 74.38% and 66.79% wells for pre-monsoon, monsoon, post-monsoon and winter seasons respectively showed increasing trends in groundwater depth. The rapid increasing trend (slope: 8.95–104.46 cm/year) in monsoon season indicates shallow groundwater resource depletion and groundwater abstraction exceeds the groundwater recharge. Moreover, dry seasons increasing trends infer that shallow pumps will not functioning in future as a result irrigation cost will increase. Although irrigated areas remain almost same (1997–2014), decreasing rainfall along with abstraction of groundwater during dry season is primarily identified as main driving force for groundwater depletion. Further study is necessary to characterize the groundwater depletion. Planned water management is urgent for ensuring sustainable irrigation water management.