This paper presents a prototype decision support system (DSS) that can be used to analyze municipal water portfolios using science-based climate models and regional scale urbanization scenarios. We present a system dynamics (SD) DSS, loosely coupled with a geographic information system (GIS) for water portfolio scenario analysis for Mesa, Arizona. The application demonstrates a multi-scale, modular, spatial framework for downscaling a regional dynamic water budget to the specific water portfolio of the City of Mesa. Climate change, population growth, surface water allocations, and groundwater supplies are calculated from WaterSim, a regional DSS developed at the Decision Center for a Desert City at Arizona State University; Mesa's specific water portfolios are generated via a portfolio module that extends the WaterSim framework to include city-scale demands, conservation estimates, "water-banking" credits, and multi-institutional constraints. The portfolio module connects a regional supply module to local and regional demand modules so that meaningful, scenario-based exploration of the city's water assets can be examined for adequacy and risk of shortages. In particular, conditions of drought, climate change, population growth, urbanization, and land-use change are simulated to reveal robust portfolio allocations that can better guarantee adequate water supplies with low cost and low risk of shortage under a broad range of conditions. Our scenario framework classifies scenario models into exogenous factors, policy options, and outcome metrics to systematically assess the key sensitivities of Mesa's water supply portfolio.