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Abstract: Combined hydro-economic models of river basins are fundamental tools for assessing management and infrastructure strategies to improve the economic efficiency of water use in a context of competition over scarce water resources. Integrated hydro-economic models have to be capable to properly reproduce the physical behavior of the system, with a realistic representation of the different surface and groundwater resources, including their interaction, and the spatial and temporal variability of resource availability. On the other hand, such models must incorporate the value of water for different urban, agricultural and industrial uses and users. Economic values for water use are defined according to the marginal residual value of water for production (for agricultural and industrial uses) or the aggregated willingness-to-pay (WTP) for urban supply and other final water uses. In this paper, we present a systematic approach to estimate the marginal economic value of surface and groundwater resources at different locations within a complex water resources system. Based on a holistic conjunctive optimization model applied to the Adra river system in Spain we asses the total and marginal opportunity costs of capacity and operation constraints, including the opportunity cost of imposing environmental constraints on water use as foreseen in future Spanish water policy following the implementation of the European Water Framework Directive. The resulting opportunity costs provide important information to water managers about economic inefficiencies of current water allocation policy or infrastructure design, and about the resource opportunity costs to be considered in the design of efficient pricing policies in regions with water scarcity issues. [Copyright &y& Elsevier]