The Constitution seems to indicate the states are sovereign
If you read the Gibbons case history, you will find that New York (and other States) were granting exclusive navigation privileges to all waters within the jurisdiction of the State to specific companies. Daniel Webster argued that the Constitution granted the power to regulate commerce to the Federal government (Article I, Section 8, Clause 3) so sovereignty over routes of commerce such as navigable waters belonged to the Federal government, and that to argue otherwise would result in confusing and contradictory local regulatory policies.
Since the Federal government has jurisdiction over navigable waters, they also own the responsibility to maintain and develop them.