The following weapons were used in the film The Abyss:
Navy SEAL Lieutenant Hiram Coffey (Michael Biehn) carries a 9x19mm SIG-Sauer P226 as his sidearm. At the time of the film's release, the P226 had just started to replace the Beretta M9 as the standard-issue sidearm of the U.S. Navy SEAL teams; thus, The Abyss is quite likely the first movie ever to depict the SIG's use by SEALs.
TRIVIA: According to the screenplay, this weapon was originally supposed to be a ".45", presumably a 1911 variant.
When he suspects a threat to the nuclear warhead, LT Hiram Coffey (Michael Biehn) takes out a MAC-10 with a detachable barrel extension and gives it to fellow SEAL Schoenick (Christopher Murphy). Later, Jammer Willis (John Bedford Lloyd) disarms the SEALs, and gives the gun to Alan "Hippy" Carnes (Todd Graff), who tries to fire it, and has it grabbed away by Cat de Vries (Leo Burmester).
TRIVIA: According to the screenplay, this weapon was originally supposed to be a "CAR-15 short-barreled assault rifle."
Colt M16A2 or AR-15A2 Sporter II
U.S. Navy personnel on board the Benthyic Explorer appear to be carrying M16 assault rifles standing in for the M16A2. The M16A2s seen in the movie appears to have a "slab side" lower receiver unit, which means that it may be either a civilian AR-15A2 semi-automatic rifle (last Model R6500 with the A2 fixed carrying handle sight) or simply an A2 upper on a full-auto M16 (SP1) lower.
In the Special Edition, two Soviet sailors were seen with AK-47s slung over their shoulders when the massive tsunami approached a Soviet naval base. It can be also seen in the war footage the aliens present to Bud when he encounters the aliens. These are not fired, and are most likely to be Hudson model gun replicas.