The intent of the U.S. Clean Water Act (CWA) is to restore and maintain the chemical, physical, and biological integrity of the nation's waters and achieve fishable and swimmable lakes, rivers, and streams. To accomplish this, the CWA aimed to eliminate pollutant discharges and restrict the dredging and filling of waters, including wetlands, to protect water quality for fish, wildlife, recreation, and human consumption. Yet, Congress did not specify which of the millions of miles of streams, rivers, and lakes would be the Waters of the United States (WOTUS), or those waters that required federal protection to achieve these goals. This definition was left to the executive branch and thereby the changing administrations to compose. In the past decade, WOTUS definitions have changed every several years, over time largely eroding to protections less than those of the mid-1980’s, ultimately creating a “Gap” between protections and CWA goals. Wetlands contain approximately ⅓ of all vertebrate animals yet are being lost three times faster than forests. Half of the world’s Groundwater Dependent Ecosystems (GDE’s) exist in areas that show declining groundwater levels. In the U.S. there are 36 mostly freshwater fish families, 9 exclusively found in headwaters, most highly endemic, and 9 families with >50% headwater associates. We review the biodiversity of unprotected waters, the intent of the U.S. CWA and international protections, the scientific consensus on needed protections, and the path towards achieving clean and diverse waters.