A term used to describe a navy or branch of a navy that specializes in operations in shallow coastal waters and rivers. This is opposed to a blue water navy. Many times brown water navies use small maneuverable craft with shallow drafts.
Update:
I recently heard that the US Navy is working on a Brown Water Submarine, that is one designed to work in shallow water such as the Mediterranean, Sea of Japan and the Red Sea. As it is now all US submarines are "blue water" boats with sonar, fire control and weapons designed for deep water. These subs are actually at a disadvantage to smaller diesel electric boats designed for shore water operations. | 
