This Article presents a comparative institutional analysis of an increasingly important type of environmental conflict—the agricultural-waste-discharge and water-land-nexus conflict—using the recent citizen suit Waterkeeper v. Hudson as a case study. The objective is to assess the resource allocation efficiency and procedural fairness of the dispute processing in Hudson. The Hudson setting involves substantial scientific complexity, including ecological interdependencies, unobservable and observable land management decisions, pollutant transport, in-stream removal, and the problem of multiple and diverse sources of water quality pollution. Although the Hudson farm does fall under a regulated point source category in a state legislative definition, not all agricultural practices on the property are regulated. Hudson and other cases are demanding clearer definition of rights allocated and duties assigned in the waterland nexus conflict.