The boat has one continuous path that takes one vanadiel day to complete.
It goes something like this:
South Landing to North Landing (Stubborn Dredvodd pops on this one)
North Landing to Central Landing
Central Landing to South Landing (First Vodyanoi pop)
South Landing to Central Landing (Second Vodyanoi pop)
Central Landing to South Landing
Repeat
If you reach the North Landing out of North Sandy, the reason it could take 45 minutes, is because the boat only comes to the North Landing once per game day. Also keep in mind, that other than the North->Central ride, you have to get off the boat, wait 1 minute and wait for the next boat to arrive. If you come across Vodyanoi on the first pop and you don't finish him, wait until the second ride and he'll be waiting for you.
Also, I've noticed from the umpteen million times that I've ridden the boat, that Phanauet Channel is the area underneath Vunkerl Inlet (S). Ride the boat in the Channel a few times and then wander around the Inlet and you'll see what I'm talking about.