I loved the pirate river battle in the Dutch East Indies in Flashman's Lady, which I believe was based on real events.
Or how about bad whether grounds the air cover over Stalingrad. Did the Nazis have a presence on the Volga? Could we get a large-scale small craft engagement?
Also, I'm surprised there wasn't more of a naval theater on the Mississippi during the Civil War. But then I guess even if confederate borders can cut out a yankee gunboat, where do they take it? Still, there could be lots more sabotage from small boats, resulting in earlier attempts to make a patrol boat, voila, small boat warfare.