An above-ground storage pit spilled about 1 million gallons of manure last weekend, with some flowing into a trout stream.
A wall of the 2.2-million gallon pit near Canton failed Sunday.
The farmer, neighbors and state workers have since emptied the remaining manure. A dirt berm also was put around the break in the wall.
MPCA officials took water samples from Donaldson Creek and Wisel Creek, a trout stream, and didn't see any dead fish. A Department of Natural Resources survey also didn't find dead fish.
The pit was built in 2011 after getting a permit from Fillmore County.
The MPCA is investigating whether any charges should be filed against the owner.