The Abyss

The weapons seen in this movie are

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MAC 10 with extended barrel

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The one in the movie didn't have a stock, though.

Sig Sauer P226

Lt. Hiram Coffey (Michael Biehn) carries a SIG Sauer P226 9mm, the standard issue pistol for the U.S. Navy SEALs.

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Sig-Sauer P226 9x19mm

I would need to see screencaps to be sure, but I remember the gun being a P220. The P226 may be used by the SEALs in real life, but the prop weapon used in the movie could have still been a P220.

The only good shots of the gun itself are pretty dark, so it is hard to tell the diameter of the barrel; but, the rounds they show during the scene when Ed Harris tries to subdue Michael Biehn are clearly 9mm FMJ's.

M16A2

Or maybe M16A1 with A2 handguard. It is seen weilded by the Bethnic Explorer's Armed QM at the scene when the underwater alien palace rises from the sea.

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M16A1 with A2 style handguards - 5.56x45mm. Not utilized this way in the real world, putting the distinctive A2 handguards on the older rifle was a method used by Movie/TV armorers to simulate A2 rifles when M16A1s were the only ones available.