You know, hundreds of nuclear weapons have been lost at sea. (I believe it was hundreds, the New York Times did a story on it late in the 1980s, early in the 1990s.) Heck, whole nuclear submarines have been lost at sea.
You know who has the resources and abilities to fish out those nuclear weapons?
Yup, Atlanteans. People who breathe water and can swim and sense things down to the depths of the sea.
Is there some arrangement in your superhero world for them to fetch out the nuclear weapons? I'm sure that they retrieve them: when the casings corrode away, the bombs are a danger to local sea life. But do they just do it, saving the bombs in a storage compartment under the sea, or do they have an arrangement with a surface organization? Like, say, a government? Or Greenpeace?
And even if they do have such an agreement, what if there is a splinter group of Atlanteans who really want the bombs? Because surface dwellers, they do a lot to muck up the oceans, between plastic and chemical pollution and oil spills. They'd be perfectly justified, in their minds, in nuking us. It wouldn't take many nukes...and they probably think that they can eliminate the surface infestation and they'll be safe down in the sea.
Except, of course, let off one nuke and certain governments get antsy and toss other nukes around, and what what a surgical strike becomes a life-ending conflagration. The oceans become uninhabitable, even for Atlanteans.
The Atlanteans have another group that's against nuking the surface dwellers, even if their reason is self-preservation.
So how do you turn the concept into an adventure?
Well, it could be a one-off where everyone's an Atlantean or can travel underwater. Or it could be a situation where the Atlantean terrorist organization has to get the bomb to its proper place for a messy detonation. It's an old bomb, liable to fall apart in the very messiest way if treated the wrong way. A Good Atlantean discovers the plot but too late to stop it in the ocean. Instead, they know where it came out of the water and the name of one person who was acting as their surface contact. First you have to find that person (who has a bomb shelter and figures he or she will ride out the conflagration). Then you have to find the people he or she hired...who are supervillains, of course: maybe the type who don't know what's in the package, maybe the type who know and don't care.
Your players find them, but the bomb has already been set. Fight the bad guys, disarm the touchy bomb, and meanwhile warn all the nuclear-capable countries that there might be a tiny incident in the area...
In the meantime your players can argue the propriety of leaving unexploded nuclear weapons in the oceans, the state of diplomatic relations with the Atlanteans, and whatever eco-things they want.
Easy. Sounds like an evening's play to me.