A court complaint filed in Gloucester City, New Jersey, said that Huff was pulled over on the Walt Whitman Bridge around 11 a.m. Tuesday.
After the officer asked about the smell of marijuana in the car, Huff handed over a container with suspected pot, and then informed the officer he had the gun in the driver side door pocket, the Delaware River Port Authority officer said in the complaint.
He faces charges for possessing the gun without a permit in New Jersey and for the magazine found with six hollow-point bullets. He also faces a disorderly persons offense for having less than 50 grams of marijuana, police said.
It wasn't immediately known if Huff had a permit for the gun in another state, but New Jersey has extremely strict gun laws and does not have reciprocal agreements with any other states. Guns being transported into the state have to be kept in the trunk of a car or in a locked container, according to the state police.
Huff's bail was set at $25,000.
The Eagles released a statement Tuesday afternoon, saying they "are aware of the incident today involving Josh Huff. At this point, we are gathering more information."
Agents for Huff did not immediately return a message from The Associated Press seeking comment.
Huff, 25, has 13 catches for 72 yards and a touchdown this season, his third with the Eagles. He also has a 98-yard kick return for a score.
Information from The Associated Press was used in this report.