The current changing climate requires the development of water–energy–food (WEF) nexus-oriented systems capable of mainstreaming climate-smart innovations into resource management. This study demonstrates the cross-sectoral impacts of climate change on interlinked sectors of water, energy, and food in Narok County, Kenya, and Vhembe District, South Africa. This study used projected hydroclimatic extremes across past, present, and future scenarios to examine potential effects on the availability and accessibility of these essential resources. The projected temperature and rainfall are based on nine dynamically downscaled Coupled Model Intercomparison Project Phase 5 (CMIP 5) of the Global Climate Models (GCMs). The model outputs were derived from two IPCC “Representative Concentration Pathways (RCPs)’’, the RCP 4.5 “moderate scenario”, and RCP 8.5 “business as usual scenario”, also defined as the addition of 4.5 W/m2 and 8.5 W/m2 radiative forcing in the atmosphere, respectively, by the year 2100. For the climate change projections, outputs from the historical period (1976–2005) and projected time intervals spanning the near future, defined as the period starting from 2036 to 2065, and the far future, spanning from 2066 to 2095, were considered. An ensemble model to increase the skill, reliability, and consistency of output was formulated from the nine models. The statistical bias correction based on quantile mapping using seven ground-based observation data from the South African Weather Services (SAWS) for Limpopo province and nine ground-based observation data acquired from the Trans-African Hydro-Meteorological Observatory (TAHMO) for Narok were used to correct the systematic biases. Results indicate downscaled climate change scenarios and integrate a modelling framework designed to depict the perceptions of future climate change impacts on communities based on questionnaires and first-hand accounts. Furthermore, the analysis points to concerted efforts of multi-stakeholder engagement, the access and use of technology, understanding the changing business environment, integrated government and private sector partnerships, and the co-development of community resilience options, including climate change adaptation and mitigation in the changing climate. The conceptual climate and WEF resource modelling framework confirmed that future climate change will have noticeable interlinked impacts on WEF resources that will impact the livelihoods of vulnerable communities. Building the resilience of communities can be achieved through transformative WEF nexus solutions that are inclusive, sustainable, equitable, and balance adaptation and mitigation goals to ensure a just and sustainable future for all.