Anything that puts more water in Lake Michigan could, in the long run, affect lower-lying areas, he said. “You don’t want to do something that would, ultimately, flood Chicago in 50 or 100 years,” Mr. Nevin said. Climate change is expected to reduce water levels still further in the long run.

The owners of the big lake boats like the Dorothy Ann and its barge, the Pathfinder, contend that the federal government has fallen down on the job of dredging these harbors, which could help compensate for the low water. “If we had the dredging, we wouldn’t have the dashes,” said Mr. Barker, president of the Interlake Steamship Company.

He said the Great Lakes ports could be properly dredged for $200 million. “Pretty much all we’re asking for is the cost of a highway interchange,” he said.

The federal government has a trust fund for harbor dredging, based on taxes on cargo. The fund is supposed to receive $1.8 billion in the 2013 fiscal year, but the Army Corps of Engineers requested to spend only $850 million of the fund, a situation that led Senator David Vitter, Republican of Louisiana, to hold up a piece of paper that read “I.O.U. $6.95 Billion,” the surplus in the fund since it was established in 1986, in a hearing with Jo-Ellen Darcy, the assistant secretary of the Army for civil works. The Water Resources Development Act, which was drafted to address many of these issues, has passed the Senate and is under consideration in the House.

Don T. Riley, a former official with the Army Corps of Engineers who works with a Washington lobbying and consulting firm, Dawson & Associates, acknowledged that the extra money could seem absurd. “You’ve got this major surplus — that just sounds so dumb not to spend at least what you take in because that’s what you’re paying for,” he said. But the corps spends only what Congress appropriates, he said, and tapping the fund is not necessarily easy: even if money has been collected, ordering it to be spent increases the appropriation for the corps, and that can be politically troublesome in times of budget cutting.

The ability of humans to fix the situation is limited, said Mr. Nevin of the International Joint Commission. “We can’t make it rain.”