Farm Runoff May Be Tied to Respiratory Illness Near Salton Sea Civil Eats

Farm Runoff May Be Tied to Respiratory Illness Near the Salton Sea

New research on California’s largest landlocked lake suggests agricultural runoff in the water is feeding ‘extreme microbes’ that can emit harmful compounds into the air. 

MECCA, CALIFORNIA - JULY 12: An aerial view of agricultural fields with the shrinking Salton Sea in the distance on July 12, 2022 near Mecca, California. According to the U.S. Drought Monitor, more than 97 percent of the state of California's land area is in at least severe drought status, with nearly 60 percent in at least extreme drought. California is now in a third consecutive year of drought amid a climate-change fueled megadrought in the Southwestern United States. (Photo by Mario Tama/Getty Images)

An aerial view of agricultural fields with the shrinking Salton Sea in the distance. Mecca, California, July 2022. (Photo credit: Mario Tama/Getty Images)

June 11, 2025 Update: new study shows the Salton Sea is releasing harmful hydrogen sulfide gas more often and at higher levels than previously measured. Also, scientists say the results suggest that a significant amount of the gas is escaping undetected.

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At the Salton Sea State Recreation Area in Southern California, the smell of rotten eggs permeates the air. The odor is hydrogen sulfide, a gas produced by microbes in water depleted of oxygen. As the Salton Sea shrinks, the stench, which used to occur periodically, now happens regularly year-round.

The impact goes beyond just a noxious smell. Community members living around the Salton Sea have reported headaches, nausea, and other issues tied to the smelly gas, according to Aydee Palomino, the environmental justice project manager at Alianza Coachella Valley, a nonprofit organization supporting communities on the sea’s northwest shore. The 35,000 community members who live closest to the sea are largely farmworkers and migrants who work in the booming farming regions to the north and south.

Palomino and others at Alianza CV are also convinced that the sea’s poor water quality is linked to the region’s air pollution, long ranked as among the worst in the nation. But studies of air quality have long focused on the dust rising from the edges of the lake rather than the water itself. As water supply from the Colorado River dwindles, exposing more of the lakebed, known as playa, that dust increases, causing respiratory issues, nosebleeds, and skin rashes, as Civil Eats reported last year. A 2024 Environmental Research study found that children living near the sea have a 24 percent asthma rate—compared to the national average of 7.7 percent.

A 2024 Environmental Research study found that children living near the sea have a 24 percent asthma rate—compared to the national average of 7.7 percent.

New evidence suggests there’s more to the story. Recent research not only supports a link between Salton Sea water and poor air quality, but also suggests that microbes in the sea may be releasing more than just hydrogen sulfide. At the biannual Salton Sea Summit in October, a dozen University of California, Riverside researchers laid out evidence to policymakers, stakeholders, and community members—as if building a courtroom case—of how extreme conditions in the sea have shaped an out-of-balance microbiome there.

The Salton Sea is twice as salty as the ocean. Moreover, levels of nitrogen and phosphorous in the sea are “magnitudes higher” than at other salt lakes due to farm runoff, said U.C. Riverside doctoral student Caroline Hung, who has conducted dozens of sampling trips to the sea and was present at the summit. Hardy microbes there may be producing compounds—in addition to hydrogen sulfide—that can harm the roughly 650,000 people who live in the sea’s airshed, in Coachella and Imperial counties.

In waters overloaded with nutrients and high salt, “we have started to see blooms of high population levels of just a few species of bacteria,” said Emma Aronson, a microbial ecologist at U.C. Riverside. These “extreme microbes” are able to thrive in the sea’s salty, oxygen-starved yet nutrient-rich waters. For example, Harmful Algal Blooms (HABs) occur when populations of algae-like cyanobacteria explode, often forming mats or greenish, foamy scum and producing toxins or other irritating compounds. Furthermore, the microbes and the compounds can become airborne (and breathable), especially when wind blows across the surface of the water, generating lake spray.

Two students wearing sun hats in a boat check a tube of collected water samplea boat on the beach of the Salton Sea

At the Salton Sea, U.C. Riverside early-career scientists Caroline Hung and Charlie Diamond take water quality samples and sediment cores to analyze for potential contaminants. (Photo credits: Tina Treude and Caroline Hung)

Toxic Airborne Microbes

Monitoring the air for microbially produced toxins near other polluted bodies of water is a growing area of research around the world. Last year, scientists at Grand Lake St. Marys, Ohio, a lake polluted by high levels of agricultural runoff, published a study that quantified the concentration of microcystins, produced by cyanobacteria, in air samples. Similar studies are underway at Lake Erie. And last year, researchers in South Korea documented cyanobacterial toxins in aerosols above a polluted freshwater body, calling them an “emerging exposure route for potential risk to environmental and human health.”

Most of the work done on aerosolized microbes has occurred in the ocean. That research shows that sea spray increases with increasing wind speed and salinity. Raymond Leibensperger, a PhD student at Scripps Institute of Oceanography, studies how aerosols in polluted water—from both sea and river spray—correspond to poor air quality and hydrogen sulfide complaints from communities. More study is needed to determine whether microbes in lake spray are taking a toll on Salton Sea communities, he says, but it could be a significant contributor.

The Salton Sea is fed by agricultural runoff from the Coachella and Imperial Valleys, billion-dollar farming regions that adjoin the sea, which produce the country’s winter salad vegetables like lettuces and broccoli, as well as citrus and dates. Colorado River water supplies, the only source of irrigation in these valleys, is declining sharply as Great Basin states are required to take steps to reduce demand.

The sea’s shrinking footprint mirrors mandatory conservation cuts. And, as the increasingly salty sea recedes, tens of thousands more acres of playa will be exposed—as will decades of pesticides already trapped in the sediments from past farm runoff. These could become airborne too, sickening humans and wildlife alike.

Agricultural Runoff as the Root Cause

An aerial satellite view of land and water, where the water is dark green/blue

Satellite images, such as this one of the Salton Sea from 2003, can be used to estimate the amount of chlorophyll-A, a green pigment that cyanobacteria uses to photosynthesize. Although not perfect, the measures reflect trends in the size of blooms in the water. (Photo credit: NASA)

At the root of a lot of the [Salton Sea] difficulties are nutrient inputs that are coming in from agriculture,” said Tim Lyons, a geochemist at U.C. Riverside, at the summit. Due to this agricultural runoff, the Salton Sea is hypereutrophic, a term scientists use to describe water bodies that contain excessive nutrients.

Ammonium sulfate fertilizer inputs are so high in the Salton Sea, Lyons said, that it has 10 times the amount of sulfate measured in seawater. As a result, blooms of gypsum, or sulfate crystals, can occur. The consequence of a gypsum or Harmful Algal Bloom is the same: Blooms cause already low oxygen levels to plummet in the Salton Sea.

Once the water is depleted of oxygen, other microbes, including those that can transform sulfate into hydrogen sulfide or produce additional harmful compounds, can flourish and become airborne. Furthermore, microbial interactions impact the water chemistry, which affects the release of metals, such as arsenic or selenium, from sediments into the water.

At the October summit, the U.C. Riverside scientists made the case that policymakers should account for all of the public health consequences of eutrophic waters when developing plans to stabilize the sea. And that may require more strategic water and air monitoring than is currently being conducted. “This isn’t rocket science,” Lyons said. Eutrophic water bodies have been studied all over the world, he added, but “sadly, they’ve been neglected at the Salton Sea.”

Overlooked Microbes Run Amok

The first indication that Salton Sea microbes may be producing an airborne irritant emerged a few years ago. In 2022, biomedical researchers exposed laboratory mice to dust collected from the lake as well as dust from the desert. The mice exposed to the Salton Sea dust developed asthma-like symptoms.

Further investigation identified the dust irritant as a compound called lipopolysaccharide, or LPS, in the Salton Sea sediments. LPS is a key component of the outer cell membrane of bacteria that protects them from threats such as antibiotics. LPS can also elicit an immune response in humans.

Keziyah Yisrael, a biomedical sciences postdoctoral fellow at U.C. Riverside, distinguishes between two types of asthma—an allergic form, most commonly helped by inhalers, and a non-allergic form of lung inflammation. The mice exposed to Salton Sea dust, particularly dust collected from the southern portion of the sea, exhibited the non-allergic form of asthma. No inflammatory response occurred when mice were exposed to dust from a canyon miles away from the sea.

“LPS itself is not toxic to cells,” Yisrael says. Instead, it appears the immune system’s hyper response to LPS is what cause inflammation and tissue damage, she said. “Our current hypothesis is that the microbes are chemically modifying [their] LPS, possibly to better withstand the increasingly extreme conditions—which elicits a stronger immune system response,” Yisrael says. She and colleagues believe that LPS is not the only cause of respiratory inflammation in Salton Sea communities, but “is a large piece of the puzzle” of what’s causing health problems in those living near the lake.

What has gone unnoticed in previous studies is that particles in the air are “not just being generated from the playa, but also from lake spray,” Aronson says. Her team confirmed that LPS in the Salton Sea can survive in aerosols emitted as lake spray, a bigger concern when winds churn the sea’s surface and can carry particles up to 30 miles away.

Additional research from U.C. Riverside suggests that respiratory hospitalizations may be associated with windblown particles originating from the Salton Sea. In a new study, Will Porter, a U.C. Riverside atmospheric scientist, and his colleagues compared observed particles from a range of nearby surfaces—including the Salton Sea—to the number of daily respiratory hospitalizations in Coachella and Imperial counties.

banner showing a radar tracking screen and the words

They found the strongest correlation occurred when winds came from the Salton Sea—especially during bloom events there. “I did not expect to see this strong of a signal,” Porter says.

The findings challenge the overarching narrative: that dust particles from the playa are the sole health concern. Rather, the sea’s microbes may also be producing airborne compounds that merit greater attention, the scientists say.

However, any direct impacts on health are not yet conclusive. “What we need is causation,” says Ryan Sinclair, an environmental microbiologist at the Loma Linda School of Public Health. “The epidemiological studies necessary to demonstrate causation simply haven’t been done yet,” he adds.

Poor Water Quality, By Design

The Salton Sea sits roughly 240 feet below sea level, a landscape depression famously filled by a dam breach in 1905. President Coolidge subsequently designated the Salton Sea an agricultural sump in 1924; in 1968, the California legislature designated the Salton Sea’s primary use as agricultural drainage.

“In our Clean Water Act terms, [the ag runoff into the Salton Sea] is essentially wastewater and that has a different standard of protection,” said Laurel Firestone, member of the California State Water Resources Control Board, at this year’s October Salton Sea Summit. For example, there are no nutrient discharge limits on the two main rivers or the agricultural drains that deliver agricultural and industrial runoff from Imperial County into the lake.

Nutrient discharge regulation occurs only at individual facilities such as wastewater treatment plants, which must have permits to discharge into the Salton Sea tributaries. The Salton Sea is a glaring example of how the Clean Water Act has failed to address agricultural pollution.

“At the root of a lot of the [Salton Sea] difficulties are nutrient inputs that are coming in from agriculture.”

Last year, the Regional Water Quality Control Board began developing a total maximum daily loads (TMDL) in a bid to regulate nutrient pollution flowing into the Salton Sea, but it will likely take years to implement. The board is also taking steps to limit pollutants and promote farming best practices to control the transport of pollutants into the rivers that flow into the Salton Sea. While these are significant changes, it will take time before they have any impact, since the sea is so polluted.

Yet the consequences of the high nutrient loads were clear decades ago, before the vast majority of the Salton Sea’s fish and bird populations plummeted. As far back as 2000, the Salton Sea was characterized by high nutrient concentrations, high algal biomass, low dissolved oxygen, massive fish kills, and noxious odors.

In general, water quality monitoring for nutrients and salinity in the Salton Sea has suffered in recent years. State agencies abandoned water quality measures between 2020 and 2023, citing that existing boat ramps no longer reached the sea. The water board received a $350,000 grant to collect water quality samples for three years, starting in July 2023, but so far sampling has only taken place in one location in the southern portion of the sea that has an accessible boat ramp. The data are not yet publicly available.

And, as playa stabilization and habitat construction projects get underway, some critical data simply aren’t being gathered. “The lack of baseline data being collected on salinity, pollutants, and overall water quality of the newly constructed habitat areas will make it difficult to assess success,” says Michael Cohen, a senior researcher at the Pacific Institute, which provides independent environmental policy analysis.

“It is impossible to get water quality data from public agencies,” says Isabella Arzeno-Soltero, an environmental scientist at UCLA, who has resorted to filing public records requests to access data.

Since 2020, university researchers and citizen scientists have been monitoring water quality and posting it online to fill the gap—including Sinclair, the environmental microbiologist at the Loma Linda School of Public Health, working with Alianza CV.

In 2023, Alianza CV also mounted a hydrogen sulfide monitor on a platform above the sea on the north side to track production of the gas. Based on their results, researchers say the state monitoring isn’t sufficient.

A graph showing Between Jan-Aug 2024, the Alianza hydrogen sulfide (H2S) monitor, mounted above the Salton Sea on the northwest side, found 214 incidents in which H2S exceeded the 30 ppb threshold set by the California Air Resources Board compared to only 42 exceedance events documented by the South Coast Air Quality Management District monitor on Torres Martinez land.

Between January and August 2024, the Alianza hydrogen sulfide (H2S) monitor, mounted directly above the Salton Sea on the northern side, found 214 incidents in which H2S exceeded the 30 ppb threshold set by the California Air Resources Board compared to only 42 such events documented by the South Coast Air Quality Management District monitor on Torres Martinez land to the northwest. (Source: Diego Centeno)

Data from the monitor differs from a hydrogen sulfide monitor run by the South Coast Air Quality Management District (SC AQMD). “Since January, our sensor has detected 200 hydrogen sulfide exceedances; the SC AQMD sensor detected only 40,” says Diego Centeno, a doctoral student working with Arzeno-Soltero at UCLA, who grew up around the Salton Sea.

The California Air Resources Board established the one-hour hydrogen sulfide standard at 30 parts per billion; anything beyond that is deemed an exceedance.  The discrepancy, they believe, is due to the fact that the SC AQMD monitor sits on land northwest of the sea, and the exceedances the Alianza monitor detects typically occur when the winds come from the north.

Arzeno-Soltero says accurate exceedance data is crucial for public health protections. Even chronic hydrogen sulfide exposures below the level authorities consider dangerous have been associated with an increased prevalence of neurological effects, including headaches, mood disorders, and depression, according to a 2023 study.

There’s even less monitoring for HABs, which can produce cyanotoxins that can cause headaches, sore throats, nausea, vomiting, and other symptoms. A pilot study conducted between September 2020 to August 2021 found at least twelve genera of cyanobacteria were detected in the nearshore Salton Sea, and at least one animal was reported dead from ingesting toxins.

Despite the report’s conclusion that the algal blooms presented “a significant health risk” from toxins, there is minimal monitoring at the state level. “Due to funding, recent Harmful Algal Bloom monitoring has only occurred before holidays when people may be recreating on the sea,” the Regional Water Quality Control Board responded in an email.

“Currently, there are no federal or state regulatory standards for cyanotoxins in recreational waters,” the board said. Participating state agencies have developed voluntary guidance for responding to HABs in recreational waters. The guidance suggests that if field screening determines cyanobacteria or cyanotoxins are present, responding organizations should collect water, scum or algal mat samples for laboratory analysis; if HABs or toxins meet or exceed trigger levels, the responding organization should report to the HABs hotline and post an advisory sign.

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A student wearing a sun hat on a mooring checks water quality samples in a polluted sea

UCLA graduate student Cruz Marquez checks the mooring for the Alianza water quality monitor in the Salton Sea. (Photo credit: Alejandra Lopez)

Roxana Chavez, a regional organizer for a women’s farmworker leadership organization, Alianza Nacional de Campesinas, Inc, says the Imperial County Division of Public Health put up a billboard in early October near her home in Desert Shores, a community on the northwest shore of the Salton Sea. The billboard explains: “In certain conditions, the water may produce toxic Harmful Algal Blooms (HABs), in which children and pets are most susceptible to illness from water contact and/or ingestion.”

It also offers a QR code that it says will be updated to reflect current water quality as yellow, orange, or red, corresponding to caution, warming, or danger, respectively. But they’ve done little else to inform the community about HABs. “We notice the smell but also the color when the water changes—it becomes more greenish,” Chavez says.

Jasmyn Phillips lives in Calipatria, on the sea’s southern end. Beyond billboards, she wants to see more effort to educate Salton Sea communities about HABs—and more consistent water quality monitoring, since the Salton Sea is such a dynamic ecosystem. “Just because there are algal blooms doesn’t necessarily mean they are producing toxins,” she says.

Looking to Nature-Based Solutions

While excess nutrients fuel the conditions that cause microbes to produce hydrogen sulfide and LPS, reducing nutrient runoff enough to make a significant difference is not likely a viable solution in the near-term because the levels are so high.

The “LPS in sea spray” hypothesis is an intriguing one that needs further research—but it’s not clear how the story ends, says Cohen. “Even if you stopped nutrient inputs immediately,” he says, “you would not see immediate benefits, and you might not see benefits for decades, because there’s too much nutrient cycling within the Salton Sea.”

Community members, including Eric Reyes, executive director of Los Amigos de la Comunidad, a nonprofit organization that aids underserved communities facing environmental injustices in Imperial County, say the lack of engagement from policymakers as well as the agricultural community is wearisome. “We have a sense of urgency that we don’t see anyone else expressing,” says Reyes.

Palomino rejects the notion that nothing can be done to soak up nutrients. “How do we preserve wetlands or construct more, so they are a nature-based solution?” she asks.

The biggest challenge: Constructing wetland habitat is expensive. Tamping down windblown dust has been a key goal of the ten-year Salton Sea Management Plan so far. Over the last two years, roughly one-third of the $750 million state and federal dollars for restoration were used to develop the first large-scale project, called the Species Conservation Habitat (SCH), to suppress dust and create ponds of less salty water to support fish and fish-eating birds, as well as wetland habitat on 4,100 acres of exposed playa. While projects like these are valid, the surrounding community is frustrated that water quality is not also on the agenda, says Palomino.

The shrinking Salton Sea is also proving to be more dynamic than the conservation projects it has taken over a decade to design and construct. At the SCH, for example, nature’s attempts to restore itself have been thwarted by slower-moving conservation measures. Wetlands have been naturally forming on exposed playa where agricultural drains no longer reach the lake. The water that now spills on the playa allows vegetation to thrive, preventing dust. But in a twist, 153 acres of those emergent wetlands were destroyed during the creation of the SCH, according to Keilani Bonis-Ericksen, a geospatial scientist at Audubon California.

This year, the SCH project got a one-time $70 million boost from the Inflation Reduction Act to expand the wetland habitat by another 750 acres. Yet Cohen anticipates the incoming federal administration could further hamper both state and federal funding levels, which will stymie progress at Salton Sea.

Two years ago, an international team of researchers explored “algae turf” farming, purposefully growing algae to soak up contaminants in the Alamo River wetlands, one of the tributaries to the Salton Sea. The algae harvest effectively removed nitrogen, phosphorus, selenium, and other metal contaminants, but it’s not clear whether similar projects will continue.

“We need to be more ambitious,” says Palomino. “I’m tired of going back to community and saying, ‘I don’t know what we can do about the water.’”

Reporting for this piece was supported by the Nova Institute for Health.

This article was updated with the name of the water quality board and the current depth of the Salton Sea.

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Virginia Gewin is a freelance science journalist who covers how humans are profoundly altering the environment – from climate change to biodiversity loss – and undertaking extraordinary endeavors to preserve nature. Her work has appeared in Nature, Popular Science, Scientific American, The Atlantic, Bloomberg, bioGraphic, Discover, Science, Washington Post, Civil Eats, Ensia, Yale e360, Modern Farmer, Portland Monthly and many others. Read more >

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