Calgary police display one of the three handguns recovered from an alleged theft from an outdoor sporting goods store. (CBC)

An employee of a Calgary outdoor sporting equipment store, where more than 50 guns have gone missing, has been arrested after a police investigation.

The weeklong probe began when police recovered a gun in Edmonton, and a second gun from a house party in southeast Calgary where suspected shots were fired on April 18. Both incidents were linked to gangs or drugs, said District 4 commander Insp. Ray Robitaille on Friday.

The National Weapons Enforcement Support Team then traced the weapons back to Wholesale Sports at 25 Heritage Way S.E. in Calgary.

On Thursday evening, police arrested a female store employee and a male accomplice who were allegedly seen stealing three handguns. The Baretta, Smith and Wesson and Taurus guns were recovered.

In a preliminary audit of the store's inventory over the last seven months when the woman was working there, Wholesale Sports discovered that 54 other handguns were unaccounted for. Police said they're focusing their investigation on locating the missing firearms.

"We're very concerned that even one firearm would make its way onto the streets unlawfully. There's no doubt in this investigation that those firearms were destined for the black market," said Robitaille.

Police arrested a woman who had been working at Calgary's Wholesale Sports for about seven months. (CBC)

"They could be internationally bound for all we know," added acting Staff Sgt. Gord Eiriksson.

"A man and woman in their 20s have been charged in connection with this file. We are awaiting the charges to be sworn, at which time we will release the names," said police in a statement. Robitaille said they face charges of weapons trafficking, theft and improper storage of firearms.

If the firearms turn out to be involved in homicides or shooting injuries, the pair could be in more trouble. "They certainly would be facing charges and depending on their knowledge, they could be considered an accomplice," said Robitaille.

There will likely be a probe into the safeguards at Wholesale Sports in conjunction with a federal chief firearms officer, he added.

Police also thanked Wholesale Sports for their assistance and for being "instrumental in the success" of the probe. The chain has six stores in Western Canada, with Calgary their flagship location.

"We are fully co-operating with the police investigation to find out exactly what happened. As soon as we were notified, we fully complied with their investigation, did anything they needed us to try and help figure out what happened and that collaboration .... and that co-operation lead to the arrests yesterday," said Natalie Dawes, a spokeswoman for Wholesale Sports.