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The Ogallala Aquifer is one of the most productive agricultural regions and is referred to as the “breadbasket of the world”. It covers approximately 225,000 square miles beneath the Great Plains region spanning the states of Texas, New Mexico, Oklahoma, Kansas, Nebraska, South Dakota, Wyoming, and Colorado. The aquifer is a major water source for the region, with its use exceeding recharge. Previous studies have documented climate changes and their impacts in the region. However, this is the first study to document temperature and precipitation changes over the entire Ogallala region from 35 General Circulation Models participating in Phase 5 of the Climate Model Intercomparison Project (CMIP5). The main study objectives were (1) to provide estimates of present and future climate change scenarios for the High Plains Aquifer, (2) to translate the temperature and precipitation changes to agro-ecosystem indicator changes for Kansas using scenario funnels, and (3) to make recommendations for water resource and ecosystem managers to enable effective planning for the future availability of ecosystem services. The temperature change ranged from −4 °C to 8 °C, while the precipitation changes were between −50% to +50% over the region. This study improves the understanding of climate change on water resources and agro-ecosystems. This knowledge can be used to evaluate similar resources where the replenishment rate is slow.