There are inland checkpoints, even on the Canadian border that search people who've been in the country for a while: http://www.washingtonexaminer.com/border-patrol-checkpoint-i....

They can even nab American citizens for drug possession:

"One of the people arrested was a U.S. citizen who fled the checkpoint and led the police on a five-mile chase. The unnamed man was arrested and charged with three felonies, including reckless driving, possessing a controlled substance, and endangering the welfare of a minor."