Medium to low enthalpy geothermal resources (MLEGRs) in various Eastern African countries, Djibouti, Ethiopia, Kenya, Uganda, Tanzania, Rwanda, and Malawi, have received little attention from policymakers in the energy sector. Policymakers from these countries prioritize developing high-enthalpy resources for electric power production. Hence, many MLEGRs remain unused since they are assumed to pose higher risks of drilling unproductive deep wells. Besides, funding institutions prioritize high-enthalpy geothermal resources. Some MLEGRs have warm-to-hot springs with considerable flow rates and chemical constituents with varying concentrations. This study introduces a novel approach, using hydrogeochemical analysis of hot spring waters and a GIS-based AHP model, to select the best direct use scenarios for the warm/hot springs emanating from MLEGRs in central and western Kenya. The model is validated by contemporary commercial usage of the hot springs and similar studies in the study area. The stable isotope analysis revealed that the hydrothermal systems in Kenya are majorly recharged by meteoric water. In contrast, Kenya Rift Valley endorheic lakes, such as Lake Naivasha, Lake Nakuru, Lake Magadi, Lake Baringo, Lake Bogoria, and Lake Turkana, partly recharge some. Hence, they pose low risks of drying up during development and exploitation for thermal energy. The over 150 hot springs in Kenya produce warm to hot water with a thermal capacity of over 275 MWt. Hence, by harnessing the hot spring resources, Kenya can raise its direct use capacity from the current 18.5 MWt to about 100–200 MWt without drilling shallow or deep wells. The hot springs best suited for domestic use and aquacultural pond heating were selected as Narosura, Majimoto, Olchorro, Kipsegon, Kijabe, and Eburru. Those best suited for spas, bathing/ swimming pools, and volcanic geotourism were Lake Bogoria, Arus, Homa Hills, and Kariandusi. Overall, Lake Bogoria, Homa Hills, and Narosura hot springs were rated the best for direct use of hot springs.