Water scarcity is a growing problem around the world, and regions such as California are working to develop diversified, interconnected, and flexible water supply portfolios. To meet their resilient water portfolio goals, water utilities and irrigation districts will need to cooperate across scales to finance, build, and operate shared water supply infrastructure. However, planning studies to date have generally focused on partnership-level outcomes (i.e., highly aggregated mean cost-benefit analyses), while ignoring the heterogeneity of benefits, costs, and risks across the individual investing partners. This study contributes an exploratory modeling analysis that tests thousands of alternative water supply investment partnerships in the Central Valley of California, using a high-resolution simulation model to evaluate the effects of new infrastructure on individual water providers. The viability of conveyance and groundwater banking investments are as strongly shaped by partnership design choices (i.e., which water providers are participating, and how do they distribute the project’s debt obligation?) as by extreme hydrologic conditions (i.e., floods and droughts). Importantly, most of the analyzed partnership structures yield highly unequal distributions of water supply and financial risks across the partners, limiting the viability of cooperative partnerships. Partnership viability is especially rare in the absence of groundwater banking facilities, or under dry hydrologic conditions, even under explicitly optimistic assumptions regarding climate change. These results emphasize the importance of high-resolution simulation models and careful partnership structure design when developing resilient water supply portfolios for institutionally complex regions confronting scarcity.