Between the drought, El Niño, and the agriculture industry, California’s water problems are becoming a significant public health problem.

California has a dirty little secret.

Between the rocky coastline and the giant sequoias seen on TV and tourist brochures lies a sprawling agricultural valley. Though it’s sometimes called the nation’s salad bowl — it grows roughly half of all the fruits, nuts, and vegetables in the United States — the Central Valley is not healthy or green.

Even before the beginning of the state’s current drought, California’s Central Valley has had heavily contaminated groundwater. Today, with less water than ever to dilute toxins like arsenic and nitrates, communities that depend on groundwater are being exposed to toxic levels of water pollution, if they have any water at all.

For at least a decade, officials have known that much of the region’s drinking water is too toxic to drink. It contains levels of nitrates and arsenic that violate both state and federal laws.

The chemicals can occur naturally, but the elevated amount of nitrates in particular is the calling card of agricultural runoff.

How bad are these chemicals? Well, arsenic is a poisoner’s traditional murder weapon. Nitrates can cause chronic oxygen deprivation. In infants, they can lead to “blue baby syndrome.” Both increase cancer risk.

More than 2 million Californians are served by local water systems that have nitrate levels higher than state or federal laws deem safe, according to a 2008 count that is, state officials said, the most recent available.

Many people scattered across the San Joaquin Valley don’t have access to any municipal water system because they live in unincorporated areas.

These people often rely on wells they drill themselves, which pull up the same contaminated water. These wells leave as many as 250,000 people at high risk of nitrate contamination, according to a 2012 government-commissioned study.

As of 2008, the number of water supplies contaminated with nitrates was rising while the amount contaminated with arsenic was ebbing. The concentrations of these toxins have almost certainly gone up significantly since then, water experts told Healthline.

With no rain to replenish it, California’s groundwater is being over-pumped, and what remains in the nearly-drained aquifers is even more contaminated. These aquifers have been damaged so badly and the land over them has collapsed so dramatically, the indentations can be seen from space.

“It’s not a new problem with the drought, but the drought has worsened the problem, through expanded overdraft of groundwater,” said Peter Gleick, Ph.D., president of the water think tank Pacific Institute.

The state doesn’t track how many who drink the contaminated water experience health problems. But community groups say people get sick and statistical probability backs the claim.

“Many residents tell stories of short- and some long-term impacts from bad water,” such as headaches and nausea, said Jenny Rempel of the Community Water Center in Visalia.

As the drought has tightened its grip on the valley, residents with contaminated wells have become the lucky ones. Almost 3,000 wells have dried up. The underground water table is too low.

“People who rely on groundwater wells have been hardest hit by water quality issues for many years, but now we’re seeing complete household water loss. But this time of extended crisis is one that’s difficult to respond to. Many have gone without any running water or even an interim solution,” Rempel said.

Some residents have gotten official help in the form of large water tanks filled with water from nearby municipal water systems. But many nearby towns don’t have enough to share.

Digging new, deeper wells isn’t an option. The drought is boom time for well diggers, who are booked solid for the next year, according to the state Office of Emergency Services’ regional administrator Eric Lamoureux.

A local news story highlighted Lala Luengas, a Tulare County woman whose well recently ran dry. Her neighbors have generously let her run a hose from their well into her kitchen. With it she can cook and clean — but it’s not safe to drink.

Residents sometimes get help buying bottled water to drink, but they may also have to pay for it out of pocket. It can cost as much as a tenth of their income, according to the Community Water Center.

As more Valley residents have lost their water supplies, Kevin Hamilton, who heads community outreach at the regional Clinica Sierra Vista, suspects some have resorted to drinking the water that agribusinesses use to irrigate crops. (The industrial wells are much deeper, and are still pulling up water.)

“When people come into the health center and they’re sick, nauseated, and not feeling well, it’s difficult for us to sort something like that out,” Hamilton said. “We don’t know, unless somebody tells us ‘I drank bad water, I drank out of the canal.’ They become afraid to tell their doctors of the things they are doing because of the stigma, but they’re going to drink something.”

Things have always been tough in the Valley, but the drought has worn locals’ resilience thin.

“The desperation has gone up,” Hamilton said. “In the past people were waiting, knowing that it would change, but the last two years it hasn’t gotten better. It’s started to get worse, so people are starting to get desperate.”

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Central Valley residents are the canaries in the coal mine of the state’s shifting climate. They’ve been hit hardest, but threats to the general population are looming.

California’s seafood industry got its first real taste of pain from the drought in recent weeks, as officials delayed the start of the season for Dungeness crab, a lucrative industry in the state. Late last week, the public health department warned residents not to eat Dungeness crab, rock crab, mussels, or clams caught in Northern California.

The problem? Toxic algae have bloomed in coastal waters, most likely as a result of the same rising concentrations of agricultural chemicals, as well as higher ocean temperatures associated with El Niño.

The algae produce neurotoxins that accumulate in shellfish and some small fish, including anchovies. People who eat exposed critters get dizzy and sick to their stomachs. Eating too much can lead to amnesia and death.

The changing water economy threatens to bring additional illnesses in coming years, according to Kelly Middleton.

Middleton counts mosquitoes and tests them for disease as director of community affairs at the Greater Los Angeles County Vector Control District.

She finds herself with a front-row seat as California becomes a much less temperate place. This year, Middleton has had her hands full with West Nile Virus, a disease never seen in California before 2003.

“Typically we see higher levels during drought years and we’re seeing that in some parts of California for sure,” she said.

The state has confirmed 570 cases of the virus this year, including 34 deaths. In general, only a fraction of cases are diagnosed and reported.

Why does a mosquito-borne illness spike during a drought? The mosquitoes and birds that carry the virus can’t find water in nature, so they seek it out closer to human communities. With closer proximity come more infections.

Unused storm drains, for example, are an appealing place for mosquitoes to make their homes.

“All summer long we have runoff that trickles down and clogs up behind leaf litter and debris and those puddles breed a lot of mosquitoes,” Middleton said.

Middleton has her eye on other, more serious diseases, too.

Two invasive species of mosquito have aggressively expanded their range in California during the drought. Though no one has gotten sick in California yet, the invading species, the yellow fever mosquito and the Asian tiger mosquito, can both spread chikungunya, dengue, and yellow fever. (These insects, unlike California’s dusk-loving native mosquitoes, bite by day.)

“Drought hasn’t seemed to impact [the mosquitoes] at all in the negative way. In fact it may even be helping because of higher temperatures, because they tend to cause more monsoonal activity to hit the L.A. basin, which drives up humidity and increases the evaporation from all of our irrigated yards. That’s really the perfect environment for these mosquitoes,” Middleton said.

Chikungunya, an illness characterized by fever and joint pain, which few had ever heard of five years ago, is marching up through Mexico ever closer to the U.S. border.

“That’s our very big concern. I think it’s inevitable that we’ll start to see some of those cases here,” Middleton said.

Gleick agreed.

“This has not just been a dry drought. It’s been a hot drought and higher temperatures expand the range of pests, especially mosquitoes. That’s a growing concern among people who worry about these things,” he said.

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The drought has forced farmers to leave thousands of fields fallow because there is not enough water to irrigate them. That has put farmworkers out of work.

Many have found themselves homeless. One group in Mendoza set up an encampment in a dry irrigation ditch.

But then something strange happened. It rained — a lot — and water again ran through the ditch. The residents scrambled to save their meager possessions.

Climatologists are predicting more rain this winter, thanks to a strong El Niño ocean current effect. Two storms already moved over the state earlier this month.

Is the nightmare over? Experts are shouting “No!” from the mountaintops.

El Niño won’t end the drought no matter how much it rains, they say. Along with needed rain, the weather pattern is expected to bring warmer temperatures. That means the state likely won’t get much winter snow over the Sierra Nevada. It is spring snowmelt that feeds the state’s reservoirs.

There’s just no way that one winter — even of the heaviest predicted rainfall — can pull California out of its historic drought.  

Rain will probably ease the crisis in the San Joaquin Valley. But after four years of catastrophic dryness, it will kick up new problems, too, first among them flooding.

Water can’t absorb as quickly into hard, dry soil. Flooding is so likely in California this winter that the Federal Emergency Management Agency (FEMA) recently advised all homeowners to buy flood insurance.

Flooding is the single worst type of natural disaster in terms of the disease, death, and economic loss it causes, according to Joan Rose, Ph.D., a water specialist in the department of fisheries and wildlife at Michigan State University. Rose has written about health effects linked to El Niño cycles.

The best predictor of disease after flooding is drought in the previous months.

“Drought causes a shortage of food. With that comes poor nutrition, following that we’ve seen some outbreaks that are more severe,” Rose said.

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There’s another scar left by the drought that will likely fester in heavy rains. In the past two years, wildfires have scorched 500,000 acres, leaving them with no vegetation to hold the soil in place.

Fires, if they burn hot enough, leave behind a layer of ashen debris that actually repels water.

It’s a recipe for landslides, according to Jonathan Godt, Ph.D., the coordinator of the landslide hazards program at the U.S. Geological Survey.

Godt pointed to the site of the Colby fire, which burned in hills that abut city streets in Glendora. The map that displays risk of serious mudslides, technically called “debris flows,” was lit up crimson.

The fire burned almost two years ago, but in drought conditions, little vegetation has returned.

“A garden variety rain storm can generate debris flow from a wildfire area,” Godt said. Trees, rocks, boulders, and ash are all swept downhill.

“It’s like wet concrete. There are very few survivors from an impact from debris flow,” he said.

State and local groups are aware of the risks. And the National Weather Service monitors the same maps, issuing warnings if rain falls on the fire zones.

But Ann Croissant, Ph.D., the president of the San Gabriel Mountains Regional Conservancy, which owns some of the land that burned in the Colby fire, says her organization wants to see the state do more than warn people to evacuate. She thinks we should actively rehabilitate fire-scarred land to prevent mudslides. But state and municipal bureaucracies can make it hard to act quickly.

“In our search to find help proactively we were met with opposition, yet nothing has been substituted as a remedy,” she said.

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It’s tempting to look at these problems as the Armageddon that climate scientists have been warning about for so long.

But there’s another way to look at it, too. It’s amazing that with a drought as severe as the one California is enduring, no one has died of thirst or starvation.

“If you were living a thousand years ago, you’d be talking probably about famine and pestilence,” said Jay Lund, Ph.D., director of the Center for Watershed Sciences at the University of California, Davis. “It’s good to step back every once in a while and make note of it.”

The drought has started conversations that may lead to solutions for some of the state’s long-standing water infrastructure problems. Los Angeles is trying to rely less on water from the state’s northern half, for example, and is expanding rainwater capture.

Many rural Central Valley communities have been agitating for years to have access to public water supplies. The drought has brought more attention to their struggles, and the state and federal governments have stepped up with grants to extend pipes or drill deep municipal wells.

Droughts are good tests. They’ll let you know the weak parts of the water system,” Lund said. “This drought has taught us a lot of lessons. It has certainly taught us about the importance of groundwater, and that’s going to help with the public health concerns.”