The M4A1 is the primary rifle 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).
AKMSU rifles are seen in the hands of Russian operatives in the premiere episode "Phase Six" (S1E01). LT Danny Green (Travis Van Winkle) takes an AKMSU off one of El Toro's men in "El Toro" (S1E05).
AK-103
Russian soldiers aboard the Soviet ship carry AK-103 assault rifles, notably in "Dead Reckoning" (S1E03), "SOS" (S1E07), and "Two Sailors Walk Into a Bar" (S1E08).
SVD Dragunov Sniper Rifle
An SVD Dragunov is seen in the hands of a Russian operative in the premiere episode "Phase Six" (S1E01).
M16A4
Some of the escaped prisoners in Guantanamo Bay are armed with M16A4 rifles in "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.
Handguns
SIG-Sauer P226 Navy
Members of the Mountain Warfare Unit are armed with the SIG-Sauer P226 Navy in the series.
Beretta 92FS
The Beretta 92FS is seen throughout the series and is the sidearm carried by CMDR Tom Chandler (Eric Dane).
Beretta Cougar
A Russian officer is armed with a Beretta Cougar in "Dead Reckoning" (S1E03). Adm. Ruskov (Ravil Isyanov) is later seen using the pistol.
Several men at a checkpoint are seen firing Mossberg 500 shotguns in Season 1's finale "No Place Like Home" (S1E10).
Machine Guns
M240B Machine Gun
An M240 machine gun is seen being fired from the Nathan James in "Phase Six" (S1E01). M240's are also mounted on Navy RHIBs.
M240D Machine Gun
A UH-60 Blackhawk helicopter can be seen fitted with two door-mounted M240D machine guns.
M60 Machine Gun
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).
Nathan James Weapons
The USS Nathan James is armed with several weapons:
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 model seen is Phalanx Block 1B CIWS, the newest version of the system. The CIWS is seen being used to ward off attacking Russian helicopters in the premiere episode "Phase Six" (S1E01).
M242 Bushmaster chaingun
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).
Other
M136 AT4
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).