Realy interesting how lyrics develop by words being misheard or mispronounced. Shallow brown, was the warning cry given by lookouts on cotton traders around the coasts of south and central America. Being mainly sub tropical rainforested areas, the rivers running through these areas are mostly dark (tannin stained) or muddy brown. This brown water emties into the sea and hugs the coastal shallows before being diluted and dispersed,also most ports are situated at rivermouths or upriver,therefore if asailor spotted brown water he could be sure he was getting into the shallows and was near a rivermouth and port.