They have been especially critical of the U.S. Army Corps of Engineers (Corps) and the U.S. Environmental Protection Agency (EPA), asserting that they administer the Section 404 program in an overzealous and inflexible manner. Wetlands: Science and Information

Scientific questions about wetlands, with answers that can be important to policymakers, include how to define wetlands; how to catalogue the rate and pattern of wetland declines and losses as well as restorations and increases; and how to assess the importance of wetland changes to broader ecosystems. Many of these values have been recognized only recently. According to its most recent report of national trends, issued in 2011, total wetland acreage in 2009 was estimated to be 110.1 million acres. In April 2008, the Bush Administration issued a report saying that more than 3.6 million acres of wetlands had been restored, protected, or improved as part of the President's program to create, improve and protect wetlands, and that the number was expected to climb to 4.5 million acres by the original date set by that program—Earth Day 2009. Selected Federal Wetlands Programs

Federal program issues include the administration of programs to protect, restore, or mitigate wetland resources (especially the Clean Water Act Section 404 program); relationships between agricultural and regulatory programs; whether all wetlands should be treated the same in federal programs, and which wetlands should be subject to regulation; and whether protecting wetlands by acres is an effective proxy for protecting wetlands based on the functions they perform and the values they provide. In addition, private property questions are raised, because almost three-quarters of the remaining wetlands are located on private lands. Some wetland protection advocates have proposed that it be replaced or greatly altered. The current nationwide permit program has few strong supporters, for differing reasons. SWANCC

An issue of long-standing controversy is whether isolated waters are properly within the jurisdiction of Section 404. According to the nonbinding guidance, the agencies would assert regulatory jurisdiction over certain waters, such as traditional navigable waters and adjacent wetlands. Some critics argued that the guidance represented over-reaching by the agencies, beyond authority provided by Congress. 2015 Revised Rule

On May 27, 2015, EPA and the Corps issued a final rule revising their regulations that define the scope of waters protected under the CWA. These lawsuits, filed by industry groups, more than half of the states, and several environmental groups (nearly 90 plaintiffs in all), will test whether the agencies' interpretation of CWA jurisdiction is consistent with the Supreme Court's rulings and whether the rule complies with substantive and procedural requirements of the CWA and other laws. Other Federal Protection Efforts

Many federal agencies have been active in wetland improvement efforts in recent years. In particular, the Fish and Wildlife Service (FWS) has been promoting the success of its Partners for Fish and Wildlife program, which Congress reauthorized through FY2011 in 2006 ( P.L. State Protection Efforts

In addition to federal programs and activities, wetlands in the United States are regulated and protected through a variety of state and local laws and regulations, as well as through initiatives and actions of nongovernmental organizations, schools and universities, and private citizens. The inclusion of wetlands in a state's definition of state waters does not give automatic protection to these waters; the state must also have some form of complementary regulatory authority, such as to issue permits. The Louisiana Experience

Much of the attention to reversing wetland loss has focused on Louisiana, where an estimated 80% of the total loss of U.S. coastal wetlands has occurred and where about 40% of U.S. coastal wetlands that remain in the lower 48 states are located (coastal wetlands are about 5% of all U.S. wetlands). More recent data paint a larger picture.
Recent Congresses have considered numerous policy topics that involve wetlands. Many reflect issues of long-standing interest, such as applying federal regulations on private lands, wetland loss rates, and restoration and creation accomplishments.
The issue receiving the greatest attention recently has been determining which wetlands should be included and excluded from requirements of the Clean Water Act (CWA), especially the Section 404 permit program that regulates waste discharges affecting wetlands, which is administered by the Army Corps of Engineers and the Environmental Protection Agency (EPA). As a result of Supreme Court rulings in 2001 and 2006 that narrowed federal regulatory jurisdiction over certain isolated wetlands, the jurisdictional reach of the permit program has also been narrowed. In 2015, EPA and the Army Corps promulgated a rule to define the scope of waters protected by the CWA. The rule revises the existing administrative definition of "waters of the United States" consistent with the Supreme Court's rulings and consistent with science concerning the interconnectedness of tributaries, wetlands, and other waters and the effects of these connections on the chemical, physical, and biological integrity of downstream waters. The rule has been controversial with groups and many Members of Congress who contend that it would vastly increase federal assertion of jurisdiction that triggers CWA regulatory requirements.
Wetland protection efforts continue to engender controversy over issues of science and policy. Topics include the rate and pattern of loss, whether all wetlands should be protected in a single fashion, the effectiveness of the current suite of laws in protecting them, and the fact that 75% of remaining U.S. wetlands are located on private lands.
Many public and private efforts have sought to mitigate damage to wetlands and to protect them through acquisition, restoration, enhancement, and creation, particularly coastal wetlands. While recent data indicate success in some restoration efforts, leading to increases in some types of wetlands in some locations, many scientists question if restored or created wetlands provide equivalent replacement for natural wetlands that contribute multiple environmental services and values.
One reason for controversies about wetlands is that they occur in a wide variety of physical forms, and the numerous values they provide, such as wildlife habitat, also vary widely. In addition, the total wetland acreage in the lower 48 states is estimated to have declined from more than 220 million acres three centuries ago to 110.1 million acres in 2009. The national policy goal of no net loss, endorsed by Administrations for the past two decades, had been reached by 2004, according to the Fish and Wildlife Service, as the rate of loss had been more than offset by net gains through expanded restoration efforts authorized in multiple laws. However, more recent data show wetlands losses of nearly 14,000 acres per year. Many protection advocates say that gains do not necessarily account for the changes in quality of the remaining wetlands, and many also view federal protection efforts as inadequate or uncoordinated. Others, who advocate the rights of property owners and development interests, characterize these efforts as too intrusive. Numerous state and local wetland programs add to the complexity of the protection effort.