This song is about a fisherman who always wanted to fish and later dies while returning his catch to his small community where he is very popular. Les Claypool of Primus, who is a fisherman himself, made up the character but drew influence from a real event.
"I was watching the news and they had talked about, 'There's this fishing boat that's gone down outside the Golden Gate Bridge," Claypool said in the book Primus, Over the Electric Grapevine
. "I believe it was a salmon boat. Apparently, it had gotten struck by a cargo ship. They played the audio of this guy calling the coast guard, and it was unbelievably haunting to hear this guy going, 'There's a ship coming through the fog! It's going to hit us! It's going to hit us!' And then that's all you hear.
I remember hearing him say, 'Oh my god, we're going down,' or something to that effect. And that was it - that was all you heard. It just gave me chills. So I thought, What would be the story of this guy?
So I built this whole story of John The Fisherman, and the notion that they get struck - I don't know if it actually says it in the song, but, "Oh my god, we're going down." It's taken from the account of this fishing vessel getting struck by a ship and it going down. And they never found anybody."