As residents in the Carolinas continued to deal with the fallout from Hurricane Florence, fears have grown over the storm’s longer-term pollution risks – from pig excrement and toxic coal ash potentially seeping into rivers and into people’s homes.

Officials said 13 “hog lagoons” – pits filled with pig waste – had overflowed in North Carolina due to the storm, with dozens more likely to follow. In South Carolina, 200,000 tons of coal ash lie in the path of the deluged Waccamaw river, which is expected to reach a record flood stage this week.

Another hog lagoon had breached in Duplin county, about 60 miles north of Wilmington, the North Carolina department of environmental quality (NCDEQ) said on Tuesday.

“An on-site inspection showed that solids remained in the lagoon,” the pork council said of the overtopped hog waste pit. The council did not mention the fate of any associated liquids.

The NCDEQ said another 13 lagoons had “overtopped” – meaning they were leaking excrement – and overtopping was likely in another 30.

There are 3,300 such lagoons in North Carolina, which is the second largest hog-farming state in the US. But the lagoons, many of which are close to rivers and low-lying land currently swamped by Florence, are now posing a threat to residents and the environment. During Hurricane Floyd, in 1999, tons of hog excrement seeped into rivers in the state, wiping out fish.

NCDEQ did not release detailed information on which lagoons had been compromised.

In Goldsboro, where many roads and homes are still underwater, a slew of hog farms are dotted along the Neuse river. Many of the smaller roads had restricted access, but it was easy to see the devastation Florence had wrought on the area. There was a fetid smell in the air, a scent familiar to many of the people who live near the farms and lagoons.

Activists have campaigned against the collection of hog waste for years. The hog industry collects the faeces before spraying it on to fields as fertiliser, creating a lingering stench. In July, Smithfield Foods, the world’s largest pork producer, was ordered to pay $473.5m to people who live near three of its North Carolina farms after residents brought a case against the issues they encountered from the sewage.

Hog waste is pumped into a lagoon at a farm where hogs are raised for Smithfield Foods Inc, near Wallace, North Carolina, in May. Photograph: Justin Cook/The Guardian

The Neuse river, which runs south-east towards the badly hit town of New Bern, was still flowing ferociously on Tuesday, and there were vast pools of standing water from the flood. Businesses, including farmland, were under about 2ft of water.

A three-hour drive south, in Conway, South Carolina, there are fears for 200,000 tons of coal ash – the waste left over from burning coal at power plants, which contains toxins including mercury and arsenic – located at a decommissioned power station.

The Waccamaw river is predicted to reach record levels later this week as floodwater flows south towards the Atlantic, potentially sweeping up and distributing toxic ash located at the Grainger generating station, which closed in 2012.

Santee Cooper, South Carolina’s state-owned electric and water utility, is scrambling to prevent a breach ahead of the Waccamaw’s expected peak of 19.9ft – almost 9ft above flood level – on Sunday.

Workers have reinforced the ash pit by placing rocks and sand and digging dykes in an attempt to divert water from the Waccamaw.

If the pit is breached, it will probably have devastating consequences. In 2014, a Duke Energy coal ash pit near Eden, North Carolina, leaked 39,000 tons of coal ash into the Dan river, coating 70 miles of the riverbank with toxic sludge and causing an estimated $300m in damage.