I grew up in the Puget Sound region and my parents had a boat. We took it into Canada occasionally, and what we did was radio Customs when we crossed into Canadian waters. They would ask where we were going, and would either arrange for a customs officer to meet us at the port we were heading to, or divert us to a specific place for inspection. It was usually just a quick glance at our passports, but occasionally they would inspect the boat.
Coming back into the US was similar. Sometimes they were busy and just told us to continue without interacting with them.
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