Adding water poly to existing ocean (empty bay)

What is the best way to add a water polygon to the existing water? For instance, a bay is “dry” and you want to add a water poly to it. It can be done, but at the interface of the new poly and the existing ocean a dark line area forms (or a line of rectangles if you are too far into the existing water, or terrain, if you are not close enough to the existing water. Is there a way of interfacing these? The Loring AK area is a good example. Look at the dark dry areas that must be filled in. Thanks for any ideas.

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