The Water-Energy-Food (WEF) nexus has become an integral component duly suited to enable sustainable development and an important tool to achieve and sustain various socioeconomic and environmental outcomes, including the 2030 Agenda for Sustainable Development Goals. The WEF nexus has become increasingly important in recent years as it can holistically address humankind's current triple challenges, including resource depletion, environmental degradation, and population growth. Socioeconomic factors such as increased population, economic development, and climate change patterns frequently induce unprecedented pressure on WEF resources. From the various climate change model simulations, the climate is likely to increase in the future, exacerbating the demand of the population to access the WEF resources and services. For effective resource planning and decision-making, the availability of WEF resources must be assessed under ongoing climate change. In this regard, this study assessed rural livelihoods, health, and wellbeing indicators within the WEF nexus framework in Vhembe District Municipality (VDM), South Africa, and Narok County, Kenya. The premise was to determine the drivers of livelihood changes by applying the analytic hierarchy process (AHP), a Multi-Criteria Decision-Making to understand the causal linkages between the WEF nexus resources and the sustainable livelihood indicators. Data collected from the literature review, questionnaire/group discussions, and field visit engagements were used to formulate and develop a matrix of indicators to assess livelihoods, health, and wellbeing. A correlation analysis based on the AHP was used to determine the linkages between WEF resources and sustainable livelihood indicators. The multivariate analysis used the correlation matrix to capture the pairwise degrees of relationship between WEF resources and sustainable livelihood indicators in the two study areas. The results show that the resources for sustainable livelihoods in VDM are more sustainable than those in Narok County. The Consistency Ratio values for Narok County and VDM were 0.046 and 0.067, respectively. The resulting composite index (0.143) classified both study sites under the lowly sustainable category. The results are important for informing policy formulation that guides timely interventions to balance socio-ecological systems.