Homuth said collecting money is big DNR priority.
"As long as they pay we're happy," he said.
But for Sweeney, of the Freshwater Society, money is a secondary issue. He said enforcing the pumping limits should be one of the agency's top concerns.
"More important than the revenue is protecting the resource," he said.
Among the over-pumpers MPR News contacted, a clear pattern emerged. While it's not a scientific sample, most permit violations appeared to be based on a misunderstanding of permit requirements.
After hearing from MPR News, administrators at St. Patrick's Catholic Church in Cedar, Minn., learned that they had reported using too much water in 2007 and adjusted their water use. As a result, the DNR will refund the church several hundred dollars in overpaid water fees for that year. But the church hasn't explained other years of over pumping.
Confusion over exactly what a state permit requires also appears to be the cause of over pumping at the Gerdau Ameristeel plant in Duluth.
The company regularly reports withdrawing more water from Lake Superior than its permit allows.
Gerdau officials said the company returns nearly all the water it takes from Superior back to the lake. So to calculate how much water the company uses, they subtract the gallons of returned water from what they pump.
Homuth said the company should reduce the amount of water they pump or seek an amended permit that increases their yearly pumping rate.
"They only think they need a permit for how much they actually consume," he said, "not how much they're pumping out of the lake, which is wrong."
DNR officials predict that better enforcement of water permit pumping levels will come with a new permit monitoring system slated to be operational later this year. When the new system is up and running and tracking over-pumpers, it should flag the DNR itself.
The agency's own data shows the DNR holds 65 water permits and has over-pumped half a dozen of them, some in multiple years.