He said that DEQ staff has seen that coal ash has left the basin and entered flood waters at the H.F. Lee plant, and is trying to determine "how much of that, if any" has entered into the Neuse River.
Governor Cooper described the effects of Hurricane Florence as epic and disastrous.
After talking to more residents in New Bern, Trump traveled nearly 15o miles southwest to Conway, South Carolina, a city of nearly 24,000 that has seen record flood levels that surpassed levels from Hurricane Matthew in 2016.
Social media users have been sharing before and after pictures of the storm's destruction on Twitter.
SC governor Henry McMaster estimated his state has already suffered $1.2bn in damage.
With the remnants of Florence finally out to sea and skies bright over rivers still swelling with muddy water, President Donald Trump visited the disaster zone, riding through soggy neighbourhoods and helping pass out warm meals at a church.
President Donald Trump walks toward Marine One outside the White House en route to see the damage from Hurricane Florence in the Carolinas on September 19, 2018.
The county has opened emergency shelters in Florence, Lake City, Johnsonville and Coward.
"I think it's incredible what we're seeing", the president added.
"So as the water approaches, this polyurethane will help protect all of the material, the earth material, that we put beneath it", said Lt. Col. Bill Matheny, who is with the South Carolina National Guard.
The Little Pee Dee has crested in some regions at over 46ft (14m) and its flooding has impacted town water supplies, officials say. Trump said 1.6 million meals have been provided in North Carolina and another 400,000 are ready for victims in SC. They will likely be closed at least until almost the end of September, according to North Carolina Department of Transportation Secretary Jim Trogdon.
The president traveled south Wednesday as the region continues to grapple with the aftermath of a storm that North Carolina Gov. Roy Cooper said was "epic". The Cape Fear river is expected to crest Sunday and remain at flood stage through early next week. In a letter he said the flooding will be the worst disaster in the state's modern history, and asked congressional leaders to hurry federal aid.
About 25 miles (40 kilometers) nearer to the SC coast, Kevin Tovornik tore out carpet and removed furniture as a preventative measure because he expected flooding at the house he has owned for 20 years in Conway, where the Waccamaw River was still rising. The utility said it could not rule out the possibility that coal ash from a dump adjacent to the plant, which formerly burned coal, might be flowing into the nearby Cape Fear River.
Cooper warned that the flooding is far from over and will get worse in places.