The transition tag for Clay will amount to $7.071 million for the 2015 season as part of the salary cap being set at $143.28 million.
The transition tag is a one-year tender offer to a player for an amount that is the average of the top 10 salaries at the position. It guarantees the original club the right to match any offer the player may receive from another team. Transition tags can be rescinded, but teams that rescind a transition tag cannot use it again until next season.
Clay, 26, battled through knee and hamstring injuries most of last season but still finished third on the team with 58 receptions for 605 yards. He also improved as a run-blocker.
He told ESPN.com in December that his goal was to re-sign with Miami.
"Just being here and knowing the guys, knowing the coaches, the city, this is definitely somewhere I want to spend the rest of my career," Clay said. "I was saying that the second I got drafted."
The Dolphins selected Clay in the sixth round in 2011. He became a full-time starter for Miami the past two seasons.
ESPN.com Dolphins reporter James Walker contributed to this report.