Water resources model development and simulation efforts have seen rapid growth in recent decades to aid evaluations and planning around water scarcity and allocation. Models are typically developed by two distinct communities: (1) large-scale hydrologic modelers emphasizing hydroclimatological processes, and (2) water systems modelers emphasizing environmental, infrastructural, and institutional features that shape water scarcity at the local basin level. This study assesses whether two representative models from these communities produce consistent insights when evaluating the water scarcity vulnerabilities in the Upper Colorado River Basin within the state of Colorado. Results showed that although the regional-scale model [model for scale adaptive river transport (MOSART)—water management (WM)] can capture the aggregate effect of all water operations in the basin, it underestimates the subbasin-scale variability in specific user’s vulnerabilities. The basin-scale water systems model [State of Colorado’s Stream Simulation Model (StateMod)] suggests a larger variance of scarcity across the basin’s water users due to its more detailed accounting of local water allocation infrastructure and institutional processes. This model intercomparison highlights potentially significant limitations of large-scale studies in seeking to evaluate water scarcity and actionable adaptation strategies, as well as ways in which basin-scale water systems model’s information can be used to better inform water allocation and shortage when used in tandem with larger-scale hydrological modeling studies.