This thesis contains modelling study of groundwater flow in the Chikwawa district, lower Shire Area in the southern regions of Malawi, in order to test out the working hypothesis that deeper groundwater circulation and dissolution of salts in subsurface sediments can explain the high groundwater salinity in parts of the Chikwawa district. There have been evidences of high salinity in Karroo system (in Red beds) and in Cretaceous rocks (in Lupata series) according to the available literature on geology, and there are hotspots located close to major faults where groundwater may discharge.The 3D groundwater flow model of the problematic area in the western part of Shire River is derived by MODFLOW (PMWIN) simulations, where hydraulic conductivity attributed to the different major rock-types and faults were assigned. The semi-distributed areal recharge for the model is calculated using the Thornthwaite water balance approach based on the three meteorological stations in the area.Despite the shortcomings, the calibrated model succeeds in producing groundwater head distribution in steady state that makes a good fit to the observations. Moreover it produces time series of groundwater table for the area in transient flow simulation. Results also show that the major faults in the area must be highly conduit and have a significant role in the groundwater flow patterns.The Mwanza fault has not been found directly as the source of the high salinities by the model. However, studying the flow line in cross sections under the possible geological scenario in which the Mwanza fault continues along the Shire River suggests that in the discharge area close to the river there may be upward groundwater flow lines through Mwanza fault. It is quite possible that these flows carry out dissolved salt and are responsible for the salinity in the hot spots.The model has a very high potential to be improved with field measurements from soil sampling to regular borehole measurements, pumping tests and geophysical studies.