The Espaņola basin is an important source for municipal and agricultural groundwater supply in Northern New Mexico. There is intensifying competition over the limited resources and growing concern about the impact of pumping on aquifer recharge and discharge and the fate of contaminants. To address these concerns, we estimate capture zones for several municipal wellfields using a three-dimensional numerical inverse model of the Espanola Basin regional aquifer. The simulated capture zones have a complex three-dimensional structure, due to geologic heterogeneity, exchange with surface waters, complex spatial distribution of groundwater recharge, and interference between pumping wells. We present sensitivity of our results to model parameter uncertainty, departures from steady-state, and uncertainty in the geology model. Parameters controlling the spatial distribution of recharge are amongst the most critical.