Developing countries such as Malawi require improved access to isotope tracer tools to better characterize and manage water resources threatened by land development, deforestation and climate change. This is the first published study to use an isotope facility developed in Malawi for this purpose, instead of relying upon sample analyses from abroad. Results from this new facility are used to evaluate an important Lake Malawi catchment in the Rift Valley. This work successfully established a stable-isotope baseline, hydrochemical signatures, and system conceptualization against which future policy change and management strategies may be measured. Precipitation isotopic composition was consistent with the Global Meteoric Water Line, but varied, confirming different precipitation systems nationally. Groundwater largely followed a Local Meteoric Water Line, with limited isotopic variation indicating predominant areal groundwater recharge, but with dry-season evaporative enrichment of groundwater near Lake Malawi. Surface-water isotopes widely varied with local precipitation, suggesting the latter accounted for wet-season river flows, but upstream dambo (complex wetlands occupying a shallow, seasonal waterlogged depression) helped sustain dry-season flows. Isotope capacity reinforced water-resource conceptualization and provenance in a hydrologically complex, but not atypical, Rift Valley system, exhibiting a noted complexity of groundwater–surface-water interactions. The latter, critical to integrated water resource management, requires more focused study, to which an expanded array of isotopes will contribute to tracking Sustainable Development Goal 6 targets. This study and future catchment studies should help underpin Malawian water-resource policy implementation on several identified fronts.

Integrated Water Resources Management (IWRM) is vital to the future of Malawi and motivates this study’s provision of the first stable isotope baseline characterization of the Shire River Basin (SRB). The SRB drains much of Southern Malawi and receives the sole outflow of Lake Malawi whose catchment extends over much of Central and Northern Malawi (and Tanzania and Mozambique). Stable isotope (283) and hydrochemical (150) samples were collected in 2017–2018 and analysed at Malawi’s recently commissioned National Isotopes Laboratory. Distinct surface water dry-season isotope enrichment and wet-season depletion are shown with minor retention of enriched signatures ascribed to Lake Malawi influences. Isotopic signatures corroborate that wet-season river flows mostly arise from local precipitation, with dry-season flows supported by increased groundwater contributions. Groundwater signatures follow a local meteoric water line of limited spread suggesting recharge by local precipitation predominantly during the peak months of the wet-season. Relatively few dry-season groundwater samples displayed evaporative enrichment, although isotopic seasonality was more pronounced in the lowlands compared to uplands ascribed to amplified climatic effects. These signatures serve as isotopic diagnostic tools that valuably informed a basin conceptual model build and, going forward, may inform key identified Malawian IWRM concerns. The isotopic baseline establishes a benchmark against which future influences from land use, climate change and water mixing often inherent to IWRM schemes may be forensically assessed. It thereby enables both source-water protection and achievement of Sustainable Development Goal 6.

With the resurgence of water-isotope tracing applications for Integrated Water Resource Management in developing countries, establishing a stable isotopic baseline is necessary. Developing countries, including Malawi, continue to struggle with the generation of consistent and long-term isotopic datasets due to non-existent or inadequate in-country water-isotope capacity. Malawi has made significant advances in its quest to establish a stable isotopic baseline through the establishment of the Malawi Network of Isotope in Precipitation. This study provides the first results for the isotopic characterization of precipitation in Malawi with a view to reinforcing understanding of the country’s hydrological cycle. Error-in-variables regression defined a Local Meteoric Water Line as δ²H = 8.0 (±0.3) δ¹⁸O + 13.0 (±2.0) using stable isotopic records of 37 monthly samples from 5 stations between 2014 and 2019. Local precipitation (isotopic composition) is consistent with global precipitation expectations, its condensation-forming process occurring under equilibrium conditions and a higher intercept (d-excess) above the 10‰ for Global Meteoric Water Line, implying that air moisture recycling significantly influences local precipitation. Wider variations observed in local precipitation isotopic signatures are largely attributed to different moisture-bearing systems and diverse geographic factors across the country. Additional stations are recommended to improve spatial coverage that, together with longer temporal records, may help understanding and resolving uncertainties such as the altitude effect. This pioneering study is expected to facilitate Malawi’s ambition to achieve integrated use and improved protection of its surface water and groundwater resources in response to mounting climate change, growing population and land-development concerns.