More plot holes...

1. They probably just found a floating barge and looted it. Barges are used in modern times to transport thousands of tons of cargo and that cargo can be anything from guns, to ammo, to alcohol, to cigarettes. When they raid the atoll, the Deacon asks if there are any smokes on it. There are none, but he wouldn't be asking if they were impossible to find. Clearly it's something they've found in the past. It's just that now the atolls are less common as everything is rusting, sinking, etc...

2. If he's using modern ammo, then the ammo is watertight and the gunpowder would not get wet. So yes, the gun could work. Some guns even fire underwater. You're thinking of black gunpowder weapons with exposed gunpowder. That indeed would not fire.

3. The gills don't matter. He would only be able to breathe underwater with them. Phytoplankton produce most of the world's oxygen anyway and they live in water. If anything, the air quality would be better since there would be far less industry expelling pollutants into the atmosphere.

4. Oceans have a major impact on climate. You've never heard of the connection between the ice caps melting and climate change?

5. Their base is an oil tanker and they distilled the oil. Distillation is not an impossible process and they had the oil not just to distill but also to use as energy to produce heat needed to distill the rest of the oil. In fact, I think they showed this in one of the scenes. They can't refine it completely, which is why they "smoke" and are called "smokers."

6. Did they resurface quickly? They cut to the part when they surface, but everything in the movie indicates they spent a long time down there. Enola got bored and the smokers had time to approach the Mariner's boat, completely surround it, board it, lay a trap for him, and hide. The Mariner spent decades diving and likely knew about decompression sickness from a combination of personal experience (having survived minor cases of it) and the numerous magazines he had stored on his boat.