My question is related to boats in an intra- provincial waterway. Waterways are federal, but Ottawa, Ontario and Gatineau Quebec share the river system. As a commercial vessel what laws would regulate the sale of alcohol on the water? Let's trow in. some marine law while we are at it. Cruise ships and small commercial boats are regulated by which province?
Riverways have very known borders
Typically, the middle of the river or the deepest part of it is deemed to be the border when the river forms the border between two territories, but at times the riverbank or beach are deemed to be the line.
If you look back to the 1950s to 80s, the River Elbe had a stretch between the GDR and FRG. Because of how the Allies and Soviets carved up Germany after WW2, the borderline was very much affixed to the river bank on the GDR side, and the water was fully within FRG territory. The FRG did not sway from that on the negotiation table. All policing in that area of the Elbe thus was in the FRG, never by the GDR.
If your ship is on the St. Laurence River, and you start in Kingston, then Federal Canadian and Ontario Provincial (and while still there: Kingston municipality) laws apply. You drive straight east and end in Clayton - and the moment you cross into the US, Federal US law and New York State law apply.
If you follow the river, Cornwall Island appears. South of it, the US-Canadian border is in the center of the river, until it meets the Land at Akwesane. Up until here, either Canadian and Ontario law applied, or US and Ney York law, depending on whether you crossed the international border or not. But now it gets interesting for municipalities:
The international border becomes irrelevant as the river is embraced by Canada on both sides, but Akwesane (right north of St. Regis) is in the Province du Quebec. The border lines here are the banks and beaches of the river and its islands: as long as you are on the water or northern bank, you are in Ontario and Ontario law applies (and their municipalities can govern). If you are on the southern bank, you're in Quebec, and many islands are also in Quebec - and Quebecois law applies, while others are in Ontario with Ontarioan laws.
This pattern continues till you end at a bay very close to Pointe Beaudette, where the land border between Quebec and Ontario on the northern riverside lies. But the river continues to be Ontario ruled till a tiny bit east of Notre-Dame-des-Rivières - at which point the line between Quebec and Ontario crosses the river straight south to Port Lewis. Or, to visualize on a map: Green is Ontario land, red is Quebec land, blue is the river that is deemed to be in Ontario, and purple is the river in Quebec.
Similarly, on the Ottawa River, the coasts of the river are already Quebec starting at the Carillon dam. Up to here, the border was in the center of the river, but starting here, everything on the river is Ontario waters till, halfway past Carillon Island, at which point the river becomes Quebecois. That's about 6 miles as the crow flies down the river!
It is upon the captain to not only ensure they know where they are, but also to have current navigation charts that include the position of borders, national just as much as international.
As for example tax laws only apply within a country, ships leaving the tax zone can at some point offer services "duty free", but that is only the case for seagoing vessels due to needing to leaving coastal waters. A famous example of such is the trip to Helgoland, 43 miles off the German coast.