Water desalination is a proposed solution for mitigating the effects of drought, soil salinization, and the ecological impacts of agricultural drainage. In this study, we assess the public and private costs and benefits of distributed desalination in the Central Valley (CV) of California. We employ environmental and economic modeling to estimate the value of reducing the salinity of irrigation water; the value of augmenting water supply under present and future climate scenarios; and the human health, environmental, and climate change damages associated with generating power to desalinate water. We find that water desalination is only likely to be profitable in 4% of the CV during periods of severe drought, and that current costs would need to decrease by 70–90% for adoption to occur on the median acre. Fossil-fuel powered desalination technologies also generate air emissions that impose significant public costs in the form of human health and climate change damages, although these damages vary greatly depending on technology. The ecosystem service benefits of reduced agricultural drainage would need to be valued between $800 and $1200 per acre-foot, or nearly the full capital and operational costs of water desalination, for the net benefits of water desalination to be positive from a societal perspective.