Conservation of freshwater systems is critical in the semi-arid Southwest where ground water and flood regimes strongly influence the abundance, composition, and structure of riparian vegetation. At the same time, these systems are in high demand for competing human uses. To address this conflict, natural scientists must evaluate how anthropogenic changes to hydrologic regimes alter ecological systems. A broad foundation of natural science information is needed for ecological valuation efforts to be successful. This paper examines how to incorporate hydrologic, vegetation, avian, and economic models into an integrated framework to determine the value of changes in ecological systems. We have developed a hydro-bio-economic framework for the San Pedro River Region in Arizona, and we are developing a similar framework for the Middle Rio Grande of New Mexico. Distinct valuation studies are being conducted for each site with benefit-transfer tests between the sites.