One big difference is we don't have a huge body of federal law, called camperly law (i.e. Admiralty Law) that governs a large body of legal issues on waterways and is a superseding authority in the issues where it does apply.
Cities, counties and states are not immune. We had the state attempt to build a 75 foot fixed bridge down here, after Katrina, and were successfully sued in Admiralty court by a boat builder whose completed boats would have been hindered in navigation under the bridge. The mayors of the two towns on either side, and the head of the state Department of Transportation, all basically were quoted in various news media as saying they didn't believe the lawsuit was going to be won by the boatbuilder.
But they were wrong. They were enjoined in federal court from building the bridge at that height. That bridge now has 95 feet of clearance.
The moral of the story being, there is a difference when it's navigable waters, local governments will attempt to violate that law (or any other law) if they feel it is in their best interest to do so, and boaters do have some rights in those areas that can't be infringed (but only if, they are willing to fight for those rights).