K, here's what I'm talking about. See this map ?
The river that comes in from the top (North) goes over the Bullworth Dam. Ships can't go that way, obviously.
The Bullworth Bay & Pirate Island have no water outlets to the left (West), so no route for a ship there.
The little stream by the Asylum (South) apparently comes out of the Mountains, so no go there.
Which leaves the river that goes under the Rail Line & the New Coventry - Blue Skies bridge to the East as the only water inlet or outlet.
That's why, in the NES Story, it is where Omar gets shot off the boat and drowns, further downstream. All water traffic HAS to come in and out here, there is just no other way.