India is the largest user of groundwater in the world, accounting for a quarter of the world’s annual groundwater extraction. In Kerala, a state in Southern India, groundwater is the drinking water source for 62% of the population. Groundwater management is vital to ensure the sustainable availability of water. However, it is complex due to uncertainties in subsurface parameters. Groundwater modeling can be used as an efficient tool to understand the regional flow as well as the hydrogeological condition of the groundwater system. The modular finite-difference groundwater flow model (MODFLOW) developed by the U.S. Geological Survey (USGS) is a widely used modular three-dimensional block-centered finite difference code used for simulating dynamic features and scenarios in groundwater systems. In this study, the Visual MODFLOW Flex 7.0 is used to simulate the flow of groundwater through aquifers in the Thuthapuzha sub-basin, a sixth-order sub-basin of the Bharathapuzha river basin Kerala’s second-largest river basin. A four-layer model covering an area of 940 km² has been prepared using Visual MODFLOW Flex 7.0. Groundwater level data of 37 wells spread over the study area has been used for the model simulation. Model design, calibration, and validation have been carried out. Boundary conditions including recharge and evapotranspiration are derived from the Soil and Water Assessment Tool (SWAT) hydrologic model. The model calibration is performed in two stages, which include steady-state calibration and transient state calibration using observed groundwater levels from 2000 - 2016. The validation is done by using observed groundwater levels from 2017 - 2019. The spatial distribution of hydraulic conductivity and storage properties are optimized using a combination of the trial-and-error method. Model performance evaluation is done using Standard Error of the Estimate, Root Mean Squared and Normalized RMS, found to be in the optimum range. The results of the model are found in good agreement with the observed groundwater level data. Therefore, the model is suitable for studying the groundwater level changes in the study area. In addition, the model can be extended to study the groundwater flow dynamics of the whole Bharathapuzha river basin and similar subbasins for the sustainable planning and management of groundwater resources.