Hi,
not sure that I fully understand the question. As I understand it well, the water area in the harbour of Amsterdam is a point in case. Here http://www.openstreetmap.org/?lat=52.41937&lon=4.76023&zoom=15&layers=M you can see how the different parts of the water do have different names.
It requires to separate the different water areas,

if it is the answer to a different question, apologies, Hugo