Shane Nault of Hill County, wanted on federal charges, was arrested on Tuesday at about 5 p.m. near Woods Bay.
Lake County Sheriff Don Bell said in a Facebook post that Nault was seen working at a business in Woods Bay by ATF agents who then notified Lake County Sheriff's deputies.
When he saw the agents, Nault, 43 years old, jumped into Flathead Lake and swam out into the bay.
A private citizen allowed deputies the use of his boat to apprehend Nault, but prior to launch, Nault swam to shore in the Driftwood Lane area.
A brief chase followed through thick brush, and Nault was arrested by a deputy near the lake shore.
Nault is being held on several warrants involving drugs, in addition to his federal warrant for federal weapons and drug trafficking violations, and local charges of resisting arrest and obstructing a peace officer involving the chase.