The design of optimal water policies between farmers, municipalities and groundwaterdependent ecosystem is analysed in a hydro-economic model with physical interactions between a confined aquifer and a shallow aquifer having a natural drainage. Based on the Pecos Basin case study, we analyse the optimal trajectories of the water tables and the water allocation between users and environment flows for the ecosystems. We also explore the consequences for the water manager to use a one-cell model instead of the two-cell model. Our results show the importance to consider hydraulic conductivities for the preservation of groundwater-dependent ecosystems.