Perhaps the intent of navigable waters was to limit the federal government's jurisdiction to their power over interstate commerce. No need to speculate though.
"Current Regulatory Definition of Waters of the U.S. 40 CFR 230.3(s) The term waters of the United States means (please note: this current definition will be replaced by the definition in the final rule effective 60 days after the final rule publication date): All waters which are currently used, or were used in the past, or may be susceptible to use in interstate or foreign commerce, including all waters which are subject to the ebb and flow of the tide;"
