Brown told The Coloradoan on Monday that he intends to resign immediately and will fight the charge.
Colorado State University police records show Brown was arrested Sunday on suspicion of driving with blood-alcohol content of .08 or more, driving under the influence or while ability impaired by alcohol or drugs, and a lane use violation.
The 56-year-old's exact blood-alcohol content wasn't immediately available.
County Clerk and Recorder Scott Doyle had kept the deputy clerk's post largely vacant during his eight years in office. Brown accepted Doyle's appointment to the job about three months ago.
Doyle is term-limited in 2014. Both Brown and Doyle are Republicans.
(Copyright 2012 by The Associated Press. All Rights Reserved.)