The nation's Section 404 permitting program, of the Clean Water Act (CWA), represents one of the longest regulatory histories of designing and implementing credit trading programs to satisfy regulatory requirements. The role and the function of in-lieu fee (ILF) programs in supporting this regulatory structure have undergone a substantial change. For the first time in the history of the Sec. 404 program, 33 CFR Part 332 and 40 CFR Part 230, Subpart J (the "2008 mitigation rule" or "rule"), prioritizes the use of off-site mitigation over on-site-mitigation. Additionally, the rule prioritizes advanced, third-party mitigation; especially as achieved through mitigation banks; over any off-site compensatory mitigation provided by ILF programs (33 CFR 332.3(b)(1)). This new regulatory environment favors the use of commercial mitigation bank credits while acknowledging that the limited permittee demand of off-site mitigation credits, in particular areas, justifies the continuing need for ILF programs (Corps and EPA 2008, p.19606,19611). This research examines how regulatory officials use ILF programs under the 2008 mitigation rule, and, it determines the extent to which ILF programs are capable of fulfilling the role envisioned for them under the 2008 mitigation rule. Simulation results indicate that commercial mitigation banks cannot meet risk adjusted returns under limited credit demand conditions. ILF programs offer some additional financial capacity to fill the void in commercial bank coverage; but, this potential is limited in low demand conditions. Furthermore, empirical case studies of a Virginia and Georgia provide evidence that regulatory officials rely on ILF programs to provide off-site compensatory mitigation almost exclusively in the absence of private credit supply, as intended in the 2008 rule. Evidence in Georgia and Virginia also indicate that, in some situations, ILF programs face difficulties in providing mitigation under the constraints of limited demand and more stringent regulatory requirements.