In May, the E.P.A. found that Enbridge had drastically underestimated the amount of oil still in the river. The agency estimated that 180,000 gallons had most likely drifted to the bottom, more than 100 times Enbridge’s projection. It has ordered Enbridge to dredge sections of the river where stubborn beads of oil remain submerged.

The dredging started on July 30, and stretches of the river are being closed again. Construction crews have rumbled onto the riverfront in nearby Comstock Township, angering residents and business owners who remain fearful of another accident.

Jason Manshum, an Enbridge spokesman, said the company was working to address the township’s concerns as it followed the orders of the E.P.A. “This is the single-largest incident in the history of our organization,” he said. “From the beginning, in July 2010, we said that we would be committed to this community and the natural environment, for as long as it would take to right the rupture that happened. About three years later to the day, we’re still here.”

Larry Bell, who owns Bell’s Brewery, one of the country’s largest craft beer makers, was shocked earlier this summer to see workers clear a staging area next to his brewery near Marshall. “We’re going to be downwind of this thing,” said Mr. Bell, who filed a lawsuit last month asserting that Enbridge did not get permission from the local condominium association to build its dredge pad.

“If those airborne contaminants come in, it’s going to get into our ingredients,” Mr. Bell said. “We see that as irreparable. They can’t compensate me for taking away my business.”

Since the spill, Enbridge has become one of the largest landowners in the area — buying out 154 residential properties within a 200-foot swath that the company determined was most affected. By many accounts, Enbridge paid a fair price and has begun to put some properties up for sale.