What procedures do I have to follow to fly a seaplane from the US to Canada?
Whenever you land in the US from a departure point not in the US, you have to land at an Airport of Entry as your first US destination airport. It does not have to be a big airport. There are plenty of Class D airports that qualify. You can verify which airports are AOEs in the US Chart Supplement. Some (big ones) are also marked as such on the sectionals.
When crossing the US border, you will need to have arranged customs clearance with the US CBP beforehand if you are landing at a small AOE. You may also need a US CBP DTOPS decal for your aircraft. Then, of course, there is the flight plan. Once you have cleared US CBP, you can fly to any other US domestic destination of your choice.
I would think that when flying into Canada, the TCCA would have similar rules.