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Conservation of freshwater ecosystems in the semi-arid southwestern USA is a critical issue as these systems support habitat for wildlife and provide consumptive use for humankind. Economists have utilized stated preference techniques to value non-marketed goods and services such as freshwater ecosystems for much of the last four decades. Recently, Boyd and Banzhaf (2007) have advocated for ecosystem accounting units to be created in valuing ecosystem services such as freshwater ecosystems. Working collectively, a team of physical and social scientists developed a set of ecological endpoints for two river regions in the southwestern USA and used these ecological endpoints in a contingent valuation survey to obtain willingness to pay values for restoration and preservation alternatives. The results demonstrate statistically significant preservation and restoration estimates for the Upper San Pedro and restoration estimates for the Middle Rio Grande ecosystems. Copyright (c) 2015 John Wiley & Sons, Ltd.