Flooding could have been much worse had the sewer not been pumped out, he said.
"We would have had some pretty serious problems on Gateway Drive," he said.
A new flood wall currently in the design stages will help make sure water doesn't back up into the water plant and flood the area.
A $16 million FEMA grant awarded to the city in August will go toward the West End Sewer Separation Project, as well as the installation of a flood wall around the water plant, construction of a storm water pump station and updated gate well structures in the existing levee that will convey overland storm water into the Des Moines River.
"We need to make sure it gets in the right place so it doesn't flood us out by keeping the water in," Heffernan said.
The city sewer department also worked in The Beach Ottumwa parking lot Thursday, pumping runoff from the oxbow lagoon so water from the south side had a place to drain.
City Public Works Director Larry Seals said thankfully John Deere Ottumwa Works donated the use of tractors to help secure the pumps from the oxbow lagoon to the river.
"We wouldn't have been able to keep up with the lagoon water without them," Seals said.
Pumps ran from the oxbow lagoon next to The Beach Ottumwa into the Des Moines River, as well as from the north-side interceptor into the river.
"Anytime you close the levee for a river flood, you close off the water behind the levee," he said. "The challenge becomes to get the interior water from the protected side into the river."
The oxbow lagoon acts as a retention basin, he said.
"This rain event was intense enough that it came up to 7 feet in the last 24-hour period," Seals said Thursday afternoon.