Cheri Burness’s dog was the first to signal something was wrong with their tap water. He stopped drinking it two weeks ago. Then Burness started feeling stomach cramps. Her 12-year-old daughter was nauseous.

“It was just getting worse every day,” said Burness.

Burness’ husband is in the US navy. Their family is among hundreds of military families living near Pearl Harbor with similar complaints after the navy’s water system somehow became contaminated by petroleum.

The problems have afflicted one of the most important navy bases in the world, home to submarines, ships and the commander of US forces in the Indo-Pacific region, and they may even threaten one of Honolulu’s most important aquifers and water sources.

Residents in navy housing this week started complaining of a fuel-like odor coming from their tap water. Some, like Burness, said they suffered from stomach pain and headaches.

On Wednesday, Hawaii’s department of health said that a sample of navy tap water from an elementary school had tested positive for petroleum product. And on Thursday, the navy announced that tests had identified petroleum in its Red Hill well, which taps into an aquifer near the base.

Rear Adm Blake Converse, Pacific Fleet deputy commander, told a town hall meeting on Thursday the navy had taken the Red Hill well offline on Sunday because it was the closest well to affected housing areas.

The navy will flush clean water through its distribution system to clear residual petroleum products from the water, Converse said, and will follow that procedure with testing to make sure the water meets Environmental Protection Agency drinking standards. The process could take four to 10 days, he said. The navy has also vowed to investigate how contaminants got into the well and prevent it from happening again, he said.

It’s still unclear how exactly the petroleum ended up in the water. But the navy on 22 November said a water and fuel mixture had leaked into a fire suppression system drain line in a tunnel at a massive fuel storage facility three miles inland of Pearl Harbor. The navy said it had removed about 14,000 gallons (53,000 liters) of the mixture, and said the liquid hadn’t leaked into the environment.

So far, the navy said, it had received calls about a fuel odor or physical ailments from 680 homes in navy housing and 270 in army housing on the navy’s water system. The department has started distributing bottled water and said Marines would set up showers and laundry facilities connected to clean water.

The army said it would help affected families move into hotels or new homes and the navy is working on a similar program. The navy is also setting up dedicated medical clinics.

Burness said she had started seeing comments on social media from military families saying their tap water smelled like fuel after her daughter complained of feeling sick.

She told her family not to drink the water and not to wash their hair and face with it. She ordered private water delivery for $120 a month. The family has mostly been eating off of plastic and paper plates and eating out.

Burness said her stomach cramps were about 85% better, but not over. Her daughter’s nausea has improved. However, both are now complaining of breathing problems.

Burness said she has been frustrated with the navy’s response, which she believes has been dismissive of families’ concerns. She pointed to a Monday email from the commander of Joint Base Pearl Harbor-Hickam that told residents the navy was testing water samples but it had no immediate indication the water wasn’t safe. His email said he and his staff were drinking the water.

“All they had to do was say: ‘We see that there’s a problem, we don’t know what it is and we’re going to do whatever it takes to find out and fix it.’ That’s all they had to do. And instead, we got: ‘Nope. Looks good. Smells fine. Bye,”’ Burness said.

Navy region Hawaii, which oversees all Navy installations in the state, said the commander’s email was sent when “numbers of concerns were still very low”.

“Since then, the navy has aggressively increased sampling, testing, communication to families and others impacted, as well as started response teams of experts to address the issues we all are facing,” the command said in a statement.

The 22 November tunnel leak was only the latest involving the Red Hill Fuel Storage Facility, a complex of 20 underground fuel tanks built during the second world war.

Environmentalists and Honolulu’s municipal water utility have expressed concerns about the aging tanks since the navy disclosed one of them had leaked 27,000 gallons (102 kiloliters) in 2014.

The tanks sit 100ft (30 meters) above an aquifer that supplies about a quarter of the water consumed in Honolulu, prompting concerns that leaks could contaminate one of the city’s most crucial water sources. This is the same aquifer tapped by the Red Hill well where the navy just detected petroleum.

Last month, the Sierra Club of Hawaii and other environmental groups called on the government to shut the tanks down.