The projected global warming is expected to affect the distribution and timing of water yields (BW) and evapotranspiration (GW) for crop production. Agricultural lands of Canadian Prairies support food to over a hundred countries worldwide and strongly depend on variable water resources. We developed a modelling framework to evaluate BW and GW availability and their likely interchange in response to global warming in Nelson River Basin (NRB), the largest basin in the Canadian Prairies. We calibrated and validated an agro-hydrologic model of the NRB using monthly streamflow and yearly spring wheat yields (SWY) for the 1987-2016 period, for which we obtained satisfactory model performance. We forced the calibrated model to project the future (2030-2099) hydrologic balance and SWY using an ensemble of climate data downscaled based on six GCMs of the CMIP6 under SSP126 and SSP585 scenarios. Our results indicated that BW and GW are interlinked through dissimilar physical processes across different ecological regions, i.e., mountains, foothills, and plains. While IPCC reported multi-model ensemble mean data shows increasing precipitation and temperature in mid-to-high latitude regions, which sound favourable for crop yields, our study showed the opposite. We found a significant decrease in BW and GW rates under extreme warm-dry years for most of the NRB in the future. Given the effects of GW and BW on crop yields, we discussed implications for future water-food security and the impacts of extreme warm-dry years on the potential export of crops and the embodied water flows from these regions.