I saw it when I was very young, so this is robotech territory, late eighties early nineties. It was post-apocalyptic IIRC, and it was largely set underwater, involving submarines.

From what I can remember it started off with a pretty pitched battle at a dock of some sort where the main characters are desperately trying to escape from. Which they eventually do aboard an aforementioned submarine.

The plot resolves around them trying to locate this underwater city, or something similar. They are pursued constantly by whomever it was who attacked them at the dock originally.

Any ideas as to what it might be?