Study region: Alberta, Canada. Study focus: The security of freshwater supplies is a growing concern worldwide. Understanding dynamics of water supply and demand is the key for sustainable planning and management of watersheds. Here we analyzed the uncertainties in water supply of Alberta by building an agro-hydrological model, which accounts for major hydrological features, geo-spatial heterogeneity, and conflicts over water-food-energy resources. We examined the cumulative effects of natural features (e.g., potholes, glaciers, climate, soil, vegetation), anthropogenic factors (e.g., dams, irrigation, industrial development), environmental flow requirements (EFR), and calibration schemes on water scarcity in the dynamics of blue and green water resources, and groundwater recharge. New hydrological insights for the region: Natural hydrologic features of the region create a unique hydrological system, which must be accurately represented in the model for reliable estimates of water supply at high spatial and temporal resolution. Accounting for EFR, increases the number of months of water scarcity and the population exposed. Severe blue water scarcity in spring and summer months was found to be due to irrigated agriculture, while in winter months it was mostly due to the demands of petroleum or other industries. We found over exploitation of the groundwater in southern subbasins and concluded that more detailed analysis on groundwater flow and connectivity is required. Our study provides a general and unified approach for similar analyses in other jurisdictions around the world.