You may remember the pictures from the water crisis five years ago in Flint, Michigan. Hundreds of angry residents holding up bottles of rust-colored water and demanding answers. Months of protests were waved off by officials who denied anything was wrong. The turning point came when a local pediatrician found conclusive proof that the children of Flint were being exposed to high levels of lead in their water and prompted the state to declare an emergency. Now, that same doctor is working to solve a mystery that still worries parents in Flint: What lasting damage did the water do to their kids? Tonight, you will hear her initial findings which she says are worse than she feared. But we begin with the legacy of Flint's water crisis.

Cars line up for bottled water in Flint, Michigan. CBS News

Once a week, hundreds of cars line up for bottled water at the Greater Holy Temple Church of God in Flint.

Sandra Jones is in command. She is a pastor's wife with the voice of a four-star general. Jones keeps the cars moving and the water coming. Each family is allowed four cases of water. On this day, they gave away 36,000 bottles.

Sharyn Alfonsi: It just strikes me. It's been five years and you're still doing this.

Sandra Jones: Five years. And-- and the thing about it is it's not lightening up. I could see it if it was lightening up. But it isn't.

It is not. The state stopped giving away bottled water two years ago because it said the water is safe. Sandra Jones relies on donations of water.

Sharyn Alfonsi: What's it been like?

Larry Marshall: It's been kinda hard…

Larry Marshall was second in line. The widowed father of four got here at 5 a.m. He's been waiting five hours for water.

Larry Marshall: Water should be a basic necessity that -- we shouldn't have to wait or stand in line for, you know. This is not a third world country. But we're living like one.

Marshall, like many in Flint, still refuses to drink tap water.

Sharyn Alfonsi: And if they come to you the city or the state and they say, "You're drinking water's safe. Are you gonna believe them?

Larry Marshall: No. They lie so much and we know they lie, and I-- when they say something, it's like-- talking to the wind, you know. I don't believe nothing they say. None of the politicians, none of them.

Flint, once a prosperous hub of the American auto industry was nearly bankrupt back in 2014. Officials hoped to save money by switching the city water source from the Great Lakes to the Flint River.

Almost immediately, residents began noticing something wasn't right. The water was rust colored and many people had rashes.

But Michigan's department of environmental quality and the city insisted the water in Flint is safe. Later, a state investigation found those officials hid the fact that the river water was not treated with chemicals that would prevent the pipes from corroding. So, for months the water ate away at Flint's old pipes, releasing lead into residents' tap water.

Dr. Mona Hanna-Attisha: They were poisoned. I mean they were poisoned by this water. They were all exposed to toxic water.

Pediatrician Dr. Mona Hanna-Attisha fought for answers to the city's water crisis. CBS News

Dr. Mona Hanna-Attisha is a pediatrician in Flint, who her patients call "Dr. Mona."

Dr. Mona is a bit of a superhero herself here because she was the first to link the water to high levels of lead in the children of Flint.

Dr. Mona Hanna-Attisha: So within a few months of-- of being on this water, General Motors, which was born in Flint, and still has plants in Flint, noticed that this water, our drinking water, was corroding their engine parts. Let's pause. Like, the drinking (LAUGH) water was corroding engine parts. So they were allowed to go back to Great Lakes water.

Sharyn Alfonsi: Didn't anybody at that point say, "If it's corroding an engine, maybe this shouldn't be going into our bodies, into our kids?"

Dr. Mona Hanna-Attisha: I mean that should have been like fire alarm bells. Like, red flags.

Sharyn Alfonsi: So what did it take before your-- it-- your eyes opened about this?

Dr. Mona Hanna-Attisha: Yeah. It-- it-- it was the word lead.

Sharyn Alfonsi: Because the word lead, when you're a physician or a pediatrician signals what in your brain?

Dr. Mona Hanna-Attisha: There is no safe level of lead. We're never supposed to expose a population or a child to lead. Because we can't do much about it. It is an irreversible neurotoxin. It attacks the core of what it means to be you, and impacts cognition-- how children think. Actually drops IQ levels. It impacts behavior, leading to things like developmental delays. And it has these life-altering consequences.

In 2015, Dr. Mona and a colleague started digging through blood test records of 1,700 Flint children. Including the kids she sees at the Hurley Children's Clinic.

The non-profit clinic serves most of Flint's kids. The city is 53% black and has one of the highest poverty rates in the country.

Dr. Mona Hanna-Attisha: So we looked at the children's blood lead levels before the water switch. And we compared them to the children's blood lead levels after the water switch. And in the areas where the water lead levels were the highest, in those parts of the city, we saw the greatest increase in children's lead levels.

Armed with the first medical evidence that kids were being exposed to lead from the water, Dr. Mona did something controversial. She quickly held a press conference to share the blood test study, before other doctors reviewed her work.

Dr. Mona Hanna-Attisha: So it was a bit of an academic no-no. Kind of a form of academic disobedience. But I l--

Sharyn Alfonsi: And you knew that?

Dr. Mona Hanna-Attisha: I-- I knew that. But, like, but there was no choice-- there was no way I was going to wait to have this this research vetted.

Samples of Flint's drinking water proved to be filled with disease-causing bacteria, carcinogens, and lead. CBS News

Two weeks later, Michigan Governor Rick Snyder ordered the water switched back to the Great Lakes and declared a state of emergency.

Rick Snyder at State of the State: I say tonight as I have before I am sorry and I will fix it.

But the damage was done. Dr. Mona estimates 14,000 kids in Flint under the age of six may have been exposed to lead in their water.

Dr. Mona Hanna-Attisha: I never should have had to do the research that literally used the blood of our children as detectors of environmental contamination.

Three years after the crisis began, the percentage of third graders in Flint who passed Michigan's standardized literacy test dropped from 41% to 10%.

Kenyatta Dotson: I'm very concerned about my children. And not only my children, but I'm concerned about the children of Flint.

Kenyatta Dotson is still fearful of the water, even though the state is spending more than $300 million to fix the water system.

The city promised to replace all 12,000 supply lines that may have been contaminated with lead by last fall. Now, they say the work won't be done until summer.

Dotson says she and her daughters will continue to use bottled water for cooking and brushing their teeth.

Kenyatta Dotson: I need time to come back to a place where I feel whole again.

Sharyn Alfonsi: You don't feel whole right now?

Kenyatta Dotson: Oh no.

Sharyn Alfonsi: Would this have happened in a rich, white suburb?

Kenyatta Dotson: Maybe it would've happened in-- in a rich, white suburb. Would it have continued for as long as it has? I don't believe so.

Flint resident Gladyes Williamson (C) holds a bottle full of contaminated water, and a clump of her hair, alongside Jessica Owens (R), holding a baby bottle full of contaminated water, during a news conference after attending a House Oversight and Government Reform Committee hearing on the Flint, Michigan water crisis on Capitol Hill February 3, 2016 in Washington, DC. Getty

We found many parents in Flint still bathe their young children with bottled water -- first warmed on the stove then brought to the tub.

Dr. Mona Hanna-Attisha: When I'm in clinic-- almost every day-- a mom asks me, "Is my kid gonna be okay"? So that's a number one kind of anxiety and-- and concern right now--

Sharyn Alfonsi: How do you answer that?

Dr. Mona Hanna-Attisha: Oh, I-- I sit down. I sometimes hold their hand. And I reassure my patients and their parents just as I would before the crisis… to keep doing everything that you're supposed to be doing to promote your children's development.

In January of 2019, she launched the Flint registry, the first comprehensive look at the thousands of kids exposed to lead in Flint. The goal of the federal and state-funded program is to track the health of those kids and get them the help they need.

The registry refers hundreds of kids to specialists who conduct 8 hours of neuro-psychological assessments of their behavior and development.

Dr. Mona shared her preliminary findings with 60 Minutes.

Before the crisis, about 15% of the kids in Flint required special education services. But of the 174 children who went through the extensive neuro-exams, specialists determined that 80% will require help for a language, learning or intellectual disorder.

Sharyn Alfonsi: What are you gonna do?

Dr. Mona Hanna-Attisha: So there's not much we can do. So there's no magic pill. There's no antidote. There's no cure. We can't take away this exposure. But incredible science has taught us that there's a lot we can do to promote the health and development of children and that's exactly what we're doing.

Through the registry, already 2,000 Flint children who were exposed to lead have been connected to services such as speech and occupational therapy, which some may need for the rest of their lives.

The City of Flint Water Plant is illuminated by moonlight on January 23, 2016 in Flint, Michigan. Brett Carlsen / Getty Images

Dr. Mona Hanna-Attisha: But we also realized that our research, our science, this data and facts was also an underestimation of the exposure.

Sharyn Alfonsi: Why underestimated?

Dr. Mona Hanna-Attisha: Because we were looking at blood lead data done as part of these surveillance programs, which are done at the ages of 1 and 2. Lead in water impacts a younger age group. It impacts the unborn.

To determine that impact, Dr. Mona turned to a novel technique developed by Dr. Manish Arora at New York's Mount Sinai Hospital. He examines baby teeth. Baby teeth begin to grow in utero.

Dr. Manish Arora: And just like growth rings in trees, every day a tooth forms a ring. And anything that we're exposed to in our diet, what we eat, what we breathe, what we drink gets trapped in those growth rings.

A laser cuts through the tooth to analyze whether lead is embedded in the growth rings of teeth. Dr. Mona has sent teeth from 49 Flint kids to be analyzed. This was a scan on the tooth of a child who was 6 months old when the water source switched in Flint.

Dr. Manish Arora: As we hit that six month mark where the--

Sharyn Alfonsi: Oh, my gosh--

Dr. Manish Arora: --water-- the water supply was change, you can see how--

Sharyn Alfonsi: Look at that.

Dr. Manish Arora: You can see how the lead levels go up and then they just keep-- keep going up as more and more lead's entering the body.

Sharyn Alfonsi: It shoots straight up.

Dr. Manish Arora: Exactly.

Sharyn Alfonsi: Wow.

For the first time, researchers can pinpoint to the day, even before birth, when a child was exposed to lead from the water and at what levels. Those early years are a critical time for brain development.

As we were following Dr. Mona's work in Flint, another American city was forced to hand out cases of water. Testing on the drinking water in Newark, New Jersey, found lead levels four times higher than the federal limit. In some places, higher than Flint. Newark officials were warned about it's water more than two years ago.

Dr. Mona Hanna-Attisha: Newark, New Jersey is like living Flint all over again. If we cannot guarantee that all kids have access to safe drinking water, not just privileged kids, but all kids have access to safe drinking water. That's just one issue. Like, who are we?

Sharyn Alfonsi: This is not isolated to Flint--

Dr. Mona Hanna-Attisha: This is-- this is an everywhere story. This is an America story.

Last month, we made another visit to Flint to check in with Sandra Jones.

She was still in command despite temperatures in the single digits. Hundreds in Flint are still coming to her church parking lot for their weekly supply of water, more than five years after the crisis began.

Produced by Guy Campanile and Lucy Hatcher. Broadcast associate, Cristina Gallotto. Edited by Matt Richman.