Cmdr. Michael Runkle was relieved of duty because of a "loss of confidence in his ability to command" following the drownings, the Navy said Wednesday.
On Feb. 26, Diver 1st Class James Reyher, 28, and Diver 2nd Class Ryan Harris, 23, drowned during a training exercise at Aberdeen Proving Ground, The Baltimore Sun reported.
Their deaths were ruled accidental, but Rear Adm. Mike Tillotson, commander of the Navy Expeditionary Combat Command, called for a preliminary hearing to determine whether two senior enlisted leaders will face manslaughter charges. The hearing is scheduled for May 21.
Officials said there were other factors involved in the decision to relieve Runkle of his duties.
"We're not trying to pinpoint this on any one particular incident," said Lt. Nathan C. Potter, a Navy spokesman.
Runkle will be reassigned elsewhere within the Navy Expeditionary Combat Command, Potter said.
It has not yet been determined whether others will face disciplinary actions or charges, Potter said.