We develop and operationalize an integrated groundwater and watershed management model using data from the Kīholo aquifer on the west coast of Hawai’i Island. Results from a numerical simulation suggest that investment in fencing (passive management) is preferred to invasive species removal (active management) if we are limited to selecting a single conservation tool. However, using both instruments jointly increases net present value relative to using either instrument independently in most cases tested, and the additional benefit of invasive species removal increases as water becomes scarcer. The general results are largely insensitive to variations in the invasive species uptake rate and recharge benefits of fencing, and in all cases, use of both instruments reduces the loss resulting from the imposition of a safe minimum standard for groundwater-dependent ecosystems more effectively than either instrument alone.