The agency said it has repeatedly found oil in sections of the Kalamazoo River.
"The dredging required by EPA's order will prevent submerged oil from migrating to downstream areas where it will be more difficult or impossible to recover," the EPA said in a statement issued Thursday.
The agency is also ordering Enbridge — proponent of the controversial Northern Gateway pipeline through northern British Columbia — to maintain sediment traps throughout the river to capture oil outside the dredge areas.
The agency gave the company 15 days to provide a work plan, and said dredging should begin this spring.
The July 2010 spill near Marshall, Michigan, has dogged the company as it proceeds through a federal review of the Northern Gateway to deliver oil sands products to a tanker port in Kitimat, B.C.
The ability to clean-up diluted bitumen from Alberta's oil sands has been raised at the hearings by project opponents.
The American environmental agency issued a searing report last year criticizing the company's spill response.
A letter sent Thursday to Rich Adams, vice-president of operations for Enbridge's U.S. operations, from EPA co-ordinator Ralph H. Dollhopf, said the oil mixed with river sediment and organic matter had turned to sludge, "making it difficult to find and recover."
EPA documents note that they met twice with company officials about the administrative order.
"Enbridge's comments challenged the validity and interpretation of the data relied upon by U.S. EPA in making its determination ...," said a 36-page response.
In it, the agency discounts Enbridge's suggestion that allowing the oil to biodegrade is the best option for dealing with the remaining oil.
Also on HuffPost