The Army Corps of Engineers breached the levee in an effort to save the town of Cairo, Illinois, sacrificing farmland across the river in Missouri.
A group of farmers whose land was flooded has sued the federal government over the move.
The US says farmers who had crop insurance will be reimbursed.
By blowing a hole in the levee on Monday night, the Corps of Engineers hoped to reduce the river level at Cairo, lessen the pressure on the flood wall over the town, and relieve the flood risk further down the Mississippi River.
At Cairo, a town of about 3,000 at the confluence of the Mississippi and Ohio rivers, the measure seemed to work, with the river level declining.
The move makes use of floodways - vast basins of land surrounded by levees that can be opened to divert flooding elsewhere.
As many as 100 homes were damaged or destroyed, and the water washed away crop prospects for the year.
"Making this decision is not easy or hard," said Maj Gen Michael Walsh, who made the call to breach the levee, according to the St Louis Post Dispatch.
"It's simply grave - because the decision leads to loss of property and livelihood, either in a floodway or in an area that was not designed to flood."
Maj Gen Walsh said it could be late summer or early autumn before the submerged land fully drains.
The National Weather Service expects record flooding further down in the Mississippi River valley in the next few weeks.
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