Waterlogging of the groundwater system is not a desirable condition, it affects the utility of water resources and resources are not fully utilized to their extent. It is required to address the problems of the waterlogged groundwater system using an efficient tools like groundwater model. The groundwater system of the plain land of Cachar is waterlogged due to heavy rainfall and its topography. MODFLOW groundwater model is utilized in the current study for the analysis of the waterlogged groundwater system of Cachar, Assam. In the model, groundwater recharge is estimated through the GEC method. The model is calibrated and validated through the PEST package of MODFLOW. The calibrated model accurately depicts the study area's groundwater system. According to model results, the system has two major inflow components: recharge and storage, two outflow components: storage out and aquifer discharge. From the analysis of model computed head and drawdown, it is revealed that groundwater is near to the ground surface and groundwater level increases with time. It concludes that the condition of the groundwater system is highly waterlogged and required some plan to control waterlogging.