California faces cycles of drought and flooding that are projected to intensify, but these extremes may impact water users across the state differently due to the region’s natural hydroclimate variability and complex institutional framework governing water deliveries. To assess these risks, this study introduces a novel exploratory modeling framework informed by paleo and climate-change based scenarios to better understand how impacts propagate through California’s complex water system. A stochastic weather generator, conditioned on tree-ring data, produces a large ensemble of daily weather sequences conditioned on drought and flood conditions under the Late Renaissance Megadrought period (1550-1580 CE). Regional climate changes are applied to this weather data and drive hydrologic projections for the Sacramento, San Joaquin, and Tulare Basins. The resulting streamflow ensembles are used in an exploratory stress test using the California Food-Energy-Water System model (CALFEWS), a highly resolved, daily model of water storage and conveyance throughout California. Results show that megadrought conditions lead to unprecedented reductions in inflows and storage at major California reservoirs. Both junior and senior water rights holders experience multi-year periods of curtailed water deliveries and complete drawdowns of groundwater assets. When megadrought dynamics are combined with climate change, risks for unprecedented depletion of reservoir storage and sustained curtailment of water deliveries across multiple years emerge. Asymmetries in risk emerge depending on water source, rights, and access to groundwater banks.