The M4A1 used by the sailors aboard the USS Nathan James. Members of the US Navy's Mountain Warfare Unit can be seen using M4A1 carbines fitted with EOTech red dot sights to defend themselves against Russian helicopters in the premiere episode "Phase Six" (S1E01). US Navy sailors including the CMDR Tom Chandler (Eric Dane) are armed with the M4A1 in "Welcome to Gitmo" (S1E02). The M4A1 also is the rifle carried by Tex (John Pyper-Ferguson) throughout Season 1, beginning with "Welcome to Gitmo" (S1E02).
In "We'll Get There" (S1E04), Sailors aboard the Nathan James use M16A4 rifles fitted with what appear to be Mk 87 Mod 1 line-throwing adapters to launch parachutes into the air in order to propel the ship forward using wind power after the engines fail. Although these line launchers are used by the US Navy and can be attached to an M16 (if the flash hider is removed), they are generally only used with the M14 due to the higher pressures generated by a 7.62x51mm blank round.
A Russian operative is seen firing what appears to be an M60 built up to resemble the M60E3 machine gun in the premiere episode "Phase Six" (S1E01).
M60E3 machine gun - 7.62x51mm NATOError creating thumbnail: File missingA Russian operative seen firing what appears to be an M60 built up to resemble the M60E3 machine gun in the premiere episode "Phase Six" (S1E01). The gun appears to have a first generation butt stock, carrying handle, barrel and front sight.
Other
Phalanx CIWS
A Phalanx CIWS are seen as one of the defensive weapons of the USS Nathan James (these sequences were actually filmed aboard the active Navy destroyer the USS Dewey). The CIWS is seen being used to ward off attacking Russian helicopters in the premiere episode "Phase Six" (S1E01).
An M242 Bushmaster chaingun can be seen as one of the weapons of the USS Nathan James and is used to ward off attacking Russian helicopters in the premiere episode "Phase Six" (S1E01).
During the attack in the Arctic, another member of the Navy's MWU riding on a snowmobile can be seen using what appears to be an M136 AT4 to shoot down one of the incoming helicopters. A Gitmo prisoner is also seen using an AT4 in "Welcome to Gitmo" (S1E02).