Groundwater pollution due to nitrogen species from various land use activities and practices is a common concern in most agricultural watersheds. Minimization of nonpoint source nitrogen pollution can be achieved by appropriate changes to land use practices to the extent of not affecting local economies that depend heavily on agricultural activities. Most prior research work focused on predicting nitrogen loading and/or fate and transport of nitrate in groundwater due to various agricultural activities. In this work, however, we propose to present a broad integrated methodology for the optimal management of nitrate contamination of ground water combining environmental assessment and economic cost evaluation through multi-criteria decision analysis. The proposed methodology incorporates an integrated physical modeling framework accounting for on-ground nitrogen loading and losses, soil nitrogen dynamics, and fate and transport of nitrate in ground water to compute the sustainable on-ground nitrogen loading such that the maximum contaminant level is not violated. A number of protection alternatives to stipulate the predicted sustainable on-ground nitrogen loading are evaluated using the decision analysis that employs the importance order of criteria approach for ranking and selection of the protection alternatives. The methodology was successfully demonstrated for the Sumas-Blaine aquifer in Washington State. The results showed the importance of using this integrated approach that predicts the sustainable on-ground nitrogen loadings and provides an insight to the economic consequences generated in satisfying the environmental constraints. The results also show that the proposed decision analysis framework, within certain limitation, is effective when selecting alternatives with competing demands.