Marks said the decision was made after Irving had visited with a specialist the past few days.
"He's obviously upset about this, and we're here to support him, support the process, moving forward with him and the rehabilitation," Marks said.
Irving missed 26 consecutive games earlier this season with a right shoulder impingement. He said the pain started during the Nets' Nov. 4 game against the New Orleans Pelicans.
Irving saw an Arizona-based specialist in December and received a cortisone shot on Dec. 24. He said at the time that he hoped the cortisone would eliminate an immediate need for surgery.
Irving returned to action Jan. 12 and played nine games before suffering a right knee sprain in a loss to the Washington Wizards on Feb. 1, which turned out to be his final game of the season.
"I think Kyrie even mentioned a couple times that he's been playing through pain," Marks said. "He's been playing, and we got to give him a lot of credit for that, pushing through. He wants to be out there with his guys. It gets to the point where you say enough is enough, and again it goes to long-term health, and the best prognosis for him right now is, let's shut him down and get this taken care of once and for all."
Irving averaged 27.4 points, 5.2 rebounds and 6.4 assists in 20 games this season.
Despite Irving's shortened season, Nets head coach Kenny Atkinson said he was able to learn that Irving "was better than I even thought" and expressed optimism for the team's future.
"Faster than I thought, more skilled than I thought, higher-level competitor than I thought, much more physical than I thought," Atkinson said of Irving. "I don't think people give him enough credit how physical he is on both ends, how active he is defensively, what an attacker he is -- that bodes really well for the future. I really love the player, and I feel like we have a really good relationship, so we're in a good place there. Obviously, you want more reps, more time with him, but we'll have time in the offseason too, obviously, to connect. And when he gets healthy, we'll work with him a little bit."
Marks said he was disappointed that he and the Nets (25-28) have gotten so little of a look at their full team during what he called "a roller-coaster ride of a season." In addition to Irving, guard Caris LeVert missed seven weeks with a right thumb injury, and forward Wilson Chandler sat out 25 games due to a suspension.
Kevin Durant, who signed a four-year contract worth up to $164 million with the Nets in the offseason, also is not expected to play this season because of a ruptured right Achilles tendon, which he suffered in Game 5 of the NBA Finals in June, his final game with the Golden State Warriors.
ESPN's Malika Andrews contributed to this report.