“I am haunted by waters,” wrote Norman Maclean in “A River Runs Through It,” his 1976 novel about growing up in a family of Montana fly fishermen. Joe Robertson was haunted by waters of a different kind—the kind that can land someone in federal prison without warning. These are “navigable waters,” which carry on their current the full force of federal power to bankrupt and jail people who meddle with them. The problem is that no one knows what they are.

Robertson, a Navy veteran who died in March at 80, spent 18 months in...