A scientist with the National Oceanic and Atmospheric Administration, NOAA, says this summer's dead zone could be as large as 8500 square miles.
That's 77 percent larger than the average size of the dead zone over the last two decades. The area develops each summer when fertilizer rich water spurs algae growth in the Gulf.
"There is no question that the Minnesota River is a big source of pollution and contributes to the dead zone in the Gulf."
NOAA's David Whitall says nitrogen is the main culprit.
"Nitrogen fluxes to the Gulf come from a lot of different sources but agriculture is in fact the largest source of nitrogen to the Mississippi," says Whitall.
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The issue of nitrogen is especially important this year because it's the main fertilizer used on the nation's corn crop.
U.S. farmers this spring planted one of their largest corn crops ever, up almost 20 percent from a year ago. Much of the increase will go to meet the demands of the ethanol industry.
Runoff from farm fields carries nitrogen into streams and rivers and eventually the Gulf of Mexico. NOAA's David Whitall says the corn-biofuels-dead zone link is one area researchers will examine as they search for answers.
"Growing corn requires relatively a lot of nitrogen compared to some other crops," says Whitall. "So if you're switching cropland from something like soybeans to corn you're going to in fact be putting more nitrogen in the environment than you have been before."
Federal researches measure the nitrogen flowing into the Gulf each spring. This year nitrogen loads were 12 percent higher than average.
Another key fertilizer, phosphorus, was up 15 percent.
When the algae blooms in the Gulf decay, the plant matter absorbs oxygen. The oxygen deprived water smothers marine life, hurting the fishing industry.
Studies have shown that the upper Mississippi River Valley is a major source of nitrogen. One study says Minnesota farmland and other nitrogen sources in the state contribute about 7 percent of the load.
Most of that comes from the Minnesota River basin, which drains the state's main corn growing area in the southern half of the state.
Lori Nelson is executive director of a group called Friends of the Minnesota Valley. Nelson says the group has worked to improve water quality in the Minnesota River for more than two decades.
"There is no question that the Minnesota River is a big source of pollution and contributes to the dead zone in the Gulf," says Nelson.
Nelson says progress is being made to clean up the river but it's slow.
Federal and state easement programs have paid farmers to take thousands of acres of cropland near the Minnesota out of production. Cities have reduced pollution in the waste water they release to the river.
Nelson says those steps are important, but more needs to be done in Minnesota and other states contributing to Mississippi River pollution.
One federal study says if ethanol production continues to expand, nitrogen loads to the Gulf could increase another 30 percent.