On Wednesday the hard-throwing closer underwent an MRI, and he was placed on the disabled list with a right elbow sprain.
Lindstrom, who has 14 saves in 16 opportunities, is on no-throw status for four weeks, and in the best-case scenario, he will be back in six weeks.
"I thought it was in the forearm, and then it started to creep [up to the elbow]," Lindstrom said. "I'm optimistic about it. Obviously, I can create velocity, but the other pitches have not been there. On the other pitches, there was some discomfort."
Right-hander Chris Leroux was called up from Double-A Jacksonville to take Lindstrom's place on the roster.
For now, manager Fredi Gonzalez will mix and match the closer role. Leo Nunez, who is dealing with a right ankle sprain, is one possibility. Left-hander Dan Meyer is another choice, as is Brian Sanches, who closed this year at Triple-A New Orleans.
If Nunez is not ready, the team may end up going by committee.
"We'll see when we get there," Gonzalez said. "Obviously, we'd like to give a guy like Nunie an opportunity, but we don't know how long he's going to be out. I don't think he will be available [on Wednesday], but hopefully tomorrow."
Lindstrom said that his arm hasn't felt right for about three weeks. He had been undergoing treatment earlier, both at home and on the road.
In the ninth inning on Tuesday, Lindstrom struggled after recording two quick outs. He entered the game with Florida ahead, 6-3, but with no one on, he allowed four straight singles. He was relieved by Sanches, who allowed the game-tying single.
Also on Wednesday, Nunez's ankle bothered him. The right-hander faced two batters in the eighth inning, and both scored. He allowed a home run to Matt Wieters and a single to Robert Andino.
"The home run, the fastball was a little up," Nunez said.
Nunez rolled his ankle in Saturday's game against the Yankees. He complained that the tape on the ankle bothered him on Tuesday.
"Yesterday, the tape hurt," he said. "I tried to throw off the practice mound. I feel better for the game today."
Lindstrom has appeared in 32 games and thrown 29 innings. In Spring Training he pitched for Team USA in the World Baseball Classic, and he experienced a rotator cuff problem that caused him to miss the rest of the Grapefruit League season.
Though he now has an elbow issue, he doesn't feel it's because of overcompensating for the shoulder injury a few months ago.
"It's tough to say. I don't think so," he said of attributing his problems to the World Baseball Classic. "I wanted to do that, regardless. Some people are skeptical, and would say it had something to do with it. Some things happen for strange reasons. I didn't think this was going to be the case today."
Lindstrom also is confident that he doesn't have any ligament or tendon damage, which could lead to Tommy John surgery.
"I don't think so. I had an MRI. [It's] inflammation. They don't want to mess with the [shoulder] joint," he said. "That's why I think they're trying to calm it down, and give me a rest. It's frustrating. I was doing everything I needed to be able to be doing to be out there on the mound. I've been battling this for three weeks, something like that."
Pitching coach Mark Wiley pointed out to Lindstrom that he'd been showing hitters too much of the ball.
"As Mark said, hitters are seeing the whole ball instead of the top of the ball because I haven't been able to create that angle and get better drive with my elbow," Lindstrom said. "For somebody to be in my position, you have to be able to throw four out of five days, five out of six."
Lindstrom has struggled in nine appearances in June, giving up seven runs in 8 1/3 innings.
On Sunday, against the Yankees, he had a similar situation to Tuesday's, but he logged the save in that 6-5 win. He entered with a three-run lead, but with two outs, he gave up two runs before working out of the jam.
"I don't know if my arm was tired at the end," he said. "I have not been able to finish my pitches, especially my secondary [pitches]."
The Marlins' bullpen already is short-handed, with Kiko Calero on the disabled list with inflammation in his right shoulder.
"I guess there is no room to ease anybody in anymore," Meyer said. "This is my first real taste of the bullpen. I'm wet behind the ears, just like a lot of people. I'm going to have to step it up, just like everybody else."