The objective of this study is to evaluate the performance of twenty-eight bias-corrected CMIP6-GCMs and project changes in climate variables for the reference period (1985–2014) and the two future periods (2035–2064 and 2065–2094) under three Shared Socioeconomic Pathways (SSP2-4.5, SSP3-7.0, and SSP5-8.5). A comprehensive rating metric (CRM), estimated from eight statistical metrics, was used to evaluate the performance of GCMs. The multi-model mean ensemble (MMME) of four carefully selected best-performing CMIP6-GCMs for each climate variable was used for projection. Compared to average historical simulations in 1985–2014, the projected mean precipitation, maximum temperature (Tmax), minimum temperature (Tmin), and relative humidity (hurs) will increase by − 2.7 − 7.7 (1.5 − 20.9) %, 0.77 − 1.57 (1.08 − 2.62) ℃, 1.44 − 2.64 (1.90 − 4.06) ℃, and 1.18–3.22 (1.64 − 6.04) % in the 2035–2064 (2065–2094) periods, respectively, under all SSPs. While solar radiation (rsds) will decline by 3.1–21.8 (3.2–24.4) W/m2 for the same period under three SSPs. The increase in projected precipitation may augment water availability in the Rift Valley Lakes Basin (RVLB). However, more intense and frequent heavy precipitation is more likely to lead to flash floods and landslides, damaging crops and infrastructures. In addition, the expected substantial rise in Tmax and Tmin will further increase evapotranspiration demand, recurrent drought, and water insecurity. To fully comprehend and respond appropriately, further research is needed to determine how these changes in climate variables affect sustainable water resources management and water security in RVLB.