The vision of the U.S. government when they passed the Clean Water Act (CWA) in 1972 was to restore and maintain the chemical, physical, and biological integrity of the nation's waters to support fishing and recreation. The U.S. Environmental Protection Agency and Army Corps of Engineers have recently made major and controversial changes to the CWA in a 2020 regulation referred to as the Navigable Waters Protection Rule. This article reviews the bipartisan history of the CWA and the historic trajectory of how “waters of the United States” are defined to provide legal jurisdiction. It then discusses the science that supported changes to the CWA made in 2015 and lack of science that supported recent changes. The 2015 Clean Water Rule was intended to be a science-based clarification of what “waters of the United States” mean to CWA regulation. That rule was based on synthesis and review of >1,200 peer-reviewed articles that served as the basis for a 408-page scientific Connectivity Report. For the recently released regulation, U.S. Environmental Protection Agency's (EPA's) Science Advisory Board wrote that EPA did not incorporate the best-available science into the rule making process and provided no “comparable body of peer-reviewed evidence” to support the proposed changes to the CWA. Furthermore, the EPA ignored science by even stating that “science cannot dictate where to draw the line between Federal and State waters.” EPA's mission is to protect human and environmental health, the Corps has a vision of “engineering solutions for our Nation's toughest challenges.” Ultimately, the EPA and the Corps have ignored their responsibilities, mission, and vision by ignoring well-established science in their mandates to protect our nation's water for current and future generations.