Mining is the backbone of industrial development in many countries. During mining, groundwater levels generally cut across the mining and has led to flooding of the mine floors hindering the progress of mining and jeopardising the safety of the working force. Most of the mines adopt depressurisation schemes to pump out the excess water that causes mine flooding. The groundwater flow during mining is usually predicted using numerical models. In the present study, the discontinuities in the lignite deposit lying above a confined aquifer was modeled using Visual MODFLOW. The results showed an increased inflow flux by 2.64 times to the confined aquifer because of the presence of discontinuities, which in turn raised the piezometric levels in the confined aquifer resulting in more pumping. A rise of 3.3 m in water level was observed in the region of discontinuity, which needs to be pumped out for safe mining. The presence of discontinuity resulted in 30% additional pumping near the discontinuous zone for carrying out safe mining operations. When recharge was given to the semi-confined aquifer overlying the discontinuous lignite layer, the downward flux to upper confined aquifer increased by 4.62 times in comparison with the case without discontinuities. Particle tracking analysis was also performed to identify the source of additional flux in the zone of discontinuity. © 2021 Elsevier B.V.