The San Joaquin Valley of California (SJV) is subject to substantial ozone air pollution. Pima cottons developed in Arizona have been introduced into the SJV, where they exhibit symptoms suggesting ozone damage. We have investigated the potential for manipulation of nitrogen fertilization to reduce the effects of ozone exposure. We characterize the effect of ozone in exposure chambers on biomass, carbohydrate allocation, and hydraulic conductance of the resulting root systems (G), and the interaction of nitrogen fertilization with ozone exposure. Ozone reduces allocation to roots and substantially reduces both biomass and K on a leaf area basis. Increasing nitrogen increases biomass but reduces relative allocation to roots, thereby decreasing K per leaf area. The optimal strategy appears to be moderately high levels of nitrogen, which allow production of substantial biomass, but not levels which favor excessive foliar development and reduce K per leaf area.