Integrating an end member catchment offers a mechanistic foundation for interpreting large basin hydrology. This critical aspect is rarely evident in Malawi’s river basin studies. This study characterizes the hydrochemistry of surface and groundwater and stable isotopes of water to gain a regional picture of how the Ruo River Transboundary Catchment (RRC) influences the Shire–Zambezi River Basin. Hydrochemistry (2013 to 2024) and stable isotope (2020 to 2022) data are used. Both Gibbs and Piper diagrams were used to interpret surface and groundwater facies and hydrogeochemical processes controlling mineralization of water. SI biplots were used to trace water sources, mixing signals, and evaporation trends. Low to moderate mineralization is noted in surface and groundwater sources, and electrical conductivity varied between 19 and 622 µS/cm and 31 and 1930 µS/cm for surface (12 sites) and groundwater (151 boreholes), respectively. Piper diagram analysis reveals a Ca-Mg-HCO3 water type dominance. Gibbs plots suggested dissolution of silicate minerals and interaction of surface and groundwater. Stable oxygen (δ18O) and hydrogen (δ2H) isotope ratios in precipitation, surface, and groundwater exhibit a similar pattern, indicating a common meteoric input, variability in moisture source, and significant interaction of surface water and groundwater. SI plots indicate mixing of precipitation, surface, and groundwater of RRC. Finally, the Ruo River at flood stage reverses the flow of the Shire River sub catchments, impacting the water quality and quantity of the Zambezi, and, therefore, should be considered an important mixing end member in the Lower Shire Basin.