A form of flags have been designed for naval battles right through the Civil War; those incorporated distinguishing marks for ships

https://landenkhus372.evercolumn.com/posts/the-history-behind-the-civil-war-flag-symbols-of-a-nation-divided-3

A number of flags have been designed for naval battles in the time of the Civil War; those covered distinguishing marks for ships engaged in fight on rivers and seas alike.