The water-energy-food (WEF) nexus is quickly becoming one of the most critical global environmental challenges of the twenty first century. However, WEF systems are inherently complex; they typically are dynamic and span multiple land or agro-ecosystems at a regional or global scale. Addressing this challenge requires a systems approach to optimal and sustainable resource management across multiple dimensions. To that end, using Pajaro Valley (California) as a case study, our research aims to (1) highlight synergies and tradeoffs in food and water production, (2) build a dynamic framework capable of examining intertemporal resource relationships, and (3) detail the steps required to develop incentive-compatible financing of the resulting management plans when benefits are not distributed uniformly across users. Using a stylized model, we find that in the long run, inland growers benefit from the halting of seawater intrusion (SWI) due to overpumping of groundwater. We also calculate that the water provided by the proposed College Lake Multi-Objective Management Program—a plan designed to halt SWI and support sustainable water and agricultural development in the region—will generate net revenue of $40-58 million per year, compared to an annualized cost of less than $3 million. An equal cost-sharing plan would be desirable if the benefit of the project exceeded $1,268 per year for each well owner. Since this may not necessarily be the case for smaller well owners, one possible alternative is to allocate costs in proportion to expected benefits for each user.