<p> We measured the physical, chemical and isotopic properties of groundwater, streams and Lake Chilwa in the Lake Chilwa Basin in southern Malawi. Our goal was to assess water quality and identify the hydrogeochemical processes that control water quality. Groundwater in the Lake Chilwa Basin are highly saline which has led to water shortages because of poor water quality. We hypothesized that the highly saline groundwater resulted from water-rock interaction. The objective of the study wasto assess the chemical evolution of the groundwater and surface water and their relationship to water-rock interactions. Groundwater from 16 boreholes, 5 stream water samples and 3 samples from Lake Chilwa were collected using standard methods and investigated for temperature, pH, electrical conductivity, total dissolved solids (TDS), major ions and stable isotopes of hydrogen and oxygen. Groundwater and Lake Chilwa water had higher ionic concentrations (e.g., HCO_3^&ndash;, Na⁺, Ca²⁺, Mg²⁺) than stream water. Ionic evolution models indicate weathering of silicate minerals as the major control of the ionic concentrations. The chemistry of water in the Lake Chilwa is markedly affected by evaporation. Concentrations of the TDS, HCO_3^&ndash; and Cl^&ndash; in many locations are above the recommended limits prescribed for drinking water by the World Health Organization (WHO). The results of this study show that the poor water quality is due to natural water-rock interactions. Because quality of streams water is adequate, and because base flow to perennial streams issupported by shallow groundwater, efforts should be made to map shallow fresh groundwater aquifers for domestic and industrial use.</p><p>