I think your waterline idea makes a lot of sense, and one I haven't seen mentioned anywhere. If it's anything as good as what you've done so far, it should be great.
Some things I've noticed on the boats around here are that the waterline itself there's a buildup of scum. Mostly algae, a bit of oil and dirt, and in the case of steel hulled boats, some rust. That would probably apply more to the top and painted waterline than the bottom (floating higher at end of mission) waterlines because at those times, the boat would have spent a lot of time at the dock. This scum doesn't happen so much when the boat is moving constantly.
The scum seems to be a brown/green colour, and about 10-30cm wide depending on latitude. The farther north the boat is stationed, the less algae grows on it.
Also, there may be some areas of the hull with barnacles or other life sticking to it. These would be small whitish or brownish rings, slightly raised and about the same size as rivets. They would be random around the hull, but often in small patches of several at a time.