A number of flags have been designed for naval battles all the way through the Civil War; these included distinguishing marks for ships

https://zionscfs876.pinehavenscope.com/posts/preserving-history-the-importance-of-reenactment-quality-civil-war-flags

A form of flags had been designed for naval battles at some stage in the Civil War; these covered distinguishing marks for ships engaged in combat on rivers and seas alike.