Hechavarria participated in batting practice, but he felt discomfort and was replaced in the starting lineup at shortstop by Chris Valaika, who batted eighth.
"He's going to be evaluated, and we should know more tomorrow, hopefully," manager Mike Redmond said. "I think he made a throw and had some discomfort in his elbow. That's why we took him out, and we should know more tomorrow."
The Marlins lost, 6-1, to the Nationals on Wednesday night, and the team is opening a four-game series at Cincinnati on Thursday. Hechavarria, meanwhile, will be examined in Miami, and it is unclear if he will be available for the road trip.
Although Valaika started at shortstop on Thursday, there is a chance second baseman Donovan Solano will play some shortstop with Valaika playing second base if Hechavarria is out for an extended period.
Since last Friday night, the Marlins have had four players scratched from the starting lineup in six days -- Giancarlo Stanton (Friday), Justin Ruggiano (Saturday), Austin Kearns (Sunday) and now Hechavarria.
Hechavarria had started the first 14 games.
In 15 games, the Marlins have had 14 different lineups.
Joe Frisaro is a reporter for MLB.com. He writes a blog, called The Fish Pond. Follow him on Twitter