Thurston County sheriff's Lt. Greg Elwin said deputies responded to the scene in the Scott Lake area south of Olympia when a man called 911 to say he had shot another man.
The shooter told deputies that he fired in self defense, but investigators believe he actually shot the other man during drug buy.
The 30-year-old man who was shot was taken to Providence St. Peter Hospital and was expected to recover.
The alleged gunman, identified as 41-year-old Darren C. Shore, was booked into jail for investigation of attempted murder.
Elwin said the alligators found by deputies were likely being used to protect the drugs. The sheriff's office is working with county Animal Services to determine what will happen to the alligators.