In Seafarers of Catan, are there any special rules for ships or harbors in lakes?
From Combination of “The Fishermen of Catan” with “Seafarers” Scenarios 


  If you include the lake, it should always be completely surrounded by
  land hexes. You must  not build ships at the lake. (Of course, if you
  use the lake as a coastal hex anyway, you may  also build ships on the
  sides facing the ocean.)


I suggest this ruling would also apply to the scenario that you described above.