Reliance on groundwater is outpacing natural replenishment, a growing imbalance that requires detailed and multi-faceted water resource understanding. This study integrated water-stable isotopes and hydrogeochemical species to examine hydrogeochemical processes during groundwater recharge and evolution in the Lake Malawi basin aquifer systems. The findings provide insights into groundwater source provenance, with non-evaporated modern precipitation dominating recharge inputs. Grouped hydrochemical facies exhibit five groundwater water types, prominently featuring Ca-Mg-HCO3. Modelled hydrogeochemical data underscore dominant silicate dissolution reactions with the likely precipitation of calcite and/or high-Mg dolomitic carbonate constrained by ion exchange. Isotope hydrology reinforces water resource system conceptualisation. Coupled isotopic-hydrogeochemical lines of evidence reveal a discernible spatial-seasonal inhomogeneity in groundwater chemical character, revealing a complex interplay of meteoric water input, evaporative effects, recharge processes, and mixing dynamics. Findings show that measurable nitrate across Malawi highlights a widespread human impact on groundwater quality and an urgent need for detailed modelling to predict future trends of nitrate in groundwater with respect to extensive fertiliser use and an ever-increasing number of pit latrines and septic systems arising from rapid population growth. This study not only refined the Lake Malawi basin aquifer systems conceptualisation but also provided isotopic evidence of groundwater and lake water mixing. This study sets a base for groundwater management and policy decisions in support of the Integrated Water Resources Management principles and Sustainable Development Goal 6 objectives for groundwater sustainability in the transboundary Lake Malawi basin.
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