On April 10, 2008, the U.S. Army Corps of Engineers (Corps) and the Environmental Protection Agency (EPA) jointly published final regulations defining standards and procedures for authorizing compensatory mitigation of impacts to aquatic resources that the Corps permits under Section 404 of the Clean Water Act (CWA). Prior to these final regulations, Section 404’s compensatory mitigation program was administered under a mish-mash of guidances, inter-agency memoranda, and other policy documents issued over the span of seventeen years. Although motivated primarily by the need to bring the program under one comprehensive regulatory framework, the final regulations also introduce ecosystem services into the mitigation decisionmaking standards for the first time by requiring that “compensatory mitigation should be located . . . where it is most likely to successfully replace lost functions and services.” Easily overlooked in the lengthy Federal Register document, this is a potentially significant development, but it is unlikely to gain policy traction without substantial research into the development of efficient and reliable wetland ecosystem service assessment methods. To help orient such research efforts, this Article provides the following: (1) background on the compensatory mitigation program and ecosystem services prior to promulgation of the final regulations; (2) an overview of how the final regulations integrate ecosystem service analysis into compensatory mitigation decisions;and (3) suggestions for a research agenda to support implementation of that feature of the rule.