We have this same discussion every year about this time. There seems to be several interpretations of what the regulations mean. In my humble opinion, there is no arbitrary line down the middle of the river or along any channel. This is how the definition of border waters is stated in the 2007 Minnesota Fishing Regulations and it is almost exactly the same in Wisconsin’s regulation:
“BORDER WATERS–WISCONSIN–MINNESOTA
The seasons and regulations listed below apply to the following waters: Mississippi River (downstream of Prescott, Wisconsin and all waters between the Burlington Northern [Wisconsin] and Chicago Milwaukee [Minnesota] railroad tracks), Lake Pepin, St. Croix River, Lake St. Croix, St. Louis River, St. Louis Bay, and Superior Bay.
Daily and possession limits are the same.”
The way I read this definition the border waters downstream of Prescott, WI lie between the two railroad tracks. On the St Croix and the other rivers noted in the regulation the borders waters are shore to shore. As long as you are between the two railroad tracks or anywhere on the St Croix or other waters, you are fishing legal border waters and as such you must follow the rules of the state in which you are licensed.
In my opinion, if you are a Wisconsin angler and you have your boat nosed up on the MN shore but you are still between the railroad tracks – you can have 3 rods out the boat and you can be fishing whatever bait is legal in WI. And if I was from WI that is exactly how I would fish the Mississippi River.
But if you WI guys don’t want to take advantage of your full legal fishing rights, go ahead. Unfortunately, I live in MN and I don’t quite have the liberal fishing rights you do. But I am fishing that stretch of river shore to shore and using everything that I am entitled to.
You don’t need to harangue me about that quote about following the regs of the state in which you are licensed. I interpret that to mean that when fishing on border waters if I have a WI license I follow WI rules and if I have a MN license I follow MN rules . In my opinion, that quote has nothing to do with defining the boundary lines between the states. It has nothing to do with staying on some side of an arbitrary boundary line running down the main channel of the river. The boundary was established in the definition of border waters, not in that quote about following state rules.
But who the hell am I. That is how I apply my personal interpretation to the Minnesota and Wisconsin fishing regulations. Bounce this interpretation off your local DNR Conservation Officer and see what he thinks. If you get a ticket – hire an attorney and see how he interprets it. If it goes to court, see how the Judge interprets it. Who knows, maybe you could run it even farther up some appeals court chain. Let us all know how it works out. 
