What's the deal with salmon?
Like many examples of governmental dysfunction, the way salmon are regulated makes more sense when you look at it closely than when you simplify it for a laugh line. The reason fishing for salmon in freshwater and fishing for salmon in saltwater get regulated by different agencies is that it's the water, not the salmon, being regulated. Brian Palmer explains:
The U.S. Fish and Wildlife Service, part of the Department of the Interior, has jurisdiction over fishermen working in inland bodies of water, while the Commerce Department's National Oceanographic and Atmospheric Administration regulates marine fishing within 200 miles of the U.S. coastline. (Fishing beyond that distance is loosely governed by various international bodies and agreements.) There's nothing crazy about this regulatory divide: Large commercial operations dominate marine fisheries, whereas freshwater fishing is largely the province of sportsmen. Monitoring stocks of ocean fish is also more expensive and complex than keeping track of the population in a river.
From a commercial fisherman's perspective, this governance structure isn't nearly as vertiginous as the president implied. Most fish fall neatly within the jurisdiction of one of the two agencies. Salmon are among a handful of fish species, along with shad and eel, that cross the regulatory boundary in the course of their regular migrations, but commercial operators hunt salmon exclusively in the ocean.
Palmer goes on to note that there's a long-running effort to create a National Oceans Agency that would coordinate oceans-related policy across all the different departments. More on that here.
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