The body was discovered around 10:00 p.m.
Police say the victim was taken into the sewer pipe and, with the water inside moving rapidly, carried to the city's sewer plant two miles away where his body was recovered.
"We know the conditions when he was actually sucked into the pipe were extreme. There were millions of gallons of water, it's an over 40-inch line," Lawrence Township Police Chief Daniel Posluszny said.
The incident took place at around 2:15 p.m. near the Delaware and Raritan Canal in Lawrence Township.
Police say the owner of the land where Shemin Nurseries, a landscaping business, is located was trying to move floodwater off the property when he opened a manhole cover and was swept away.
Two other crewmembers were almost swallowed into the drain, too, but other workers were able to grab onto them and pulled them back to safety.
"No one should be opening any manhole covers to drain water, it's not an appropriate method of releasing water. There's a whole hosts of reasons why you're not supposed to do that," Chief Posluszny said.
Throughout the evening, crews worked quickly on backhoes as large vehicles were brought in to help pump water out of the line.
During the search, a jet ski was used in case the missing man was to surface in the canal.
Cameras were used in several spots to see if the man was able to find an air pocket.
Prior to the man's body being recovered, the police chief said the rescue effort was becoming dangerous.
"There's still quite a bit of water in there so a search of just going entirely through the area is not going to be beneficial, it's going to be dangerous for the firefighters going through," Posluszny said.
Neighbors say their street was majorly hit by flooding because of Hurricane Irene.
Bakers Basin Road was covered in floodwater all the way past Route 1.
As for the victim, his name has not been released.