With the rapid growth of Federal naval forces 1861-1862 manpower became a critical issue. Gen. U.S. Grant mentions the policy of providing manpower for the river fleets, under naval command, from army ranks. A practical fellow, that Grant. You might want to read his Memoirs, mention made in the Tennessee Campaign of Army-Navy cooperation in operations.

The National Archives have all of the records that would be specific to a search of your ancestor. I've found them to be difficult to communicate with; repeated communication regarding enquiry might be necessary.