Researchers Jeff Crooks and Stephany Garcia checked the minnow traps left at the murky mouth of the Tijuana River on a sunny October morning.

They didn’t expect any catches. They haven’t had any for months. The estuary at the southern edge of California, which borders Mexico, has been too polluted with untreated wastewater and sedimentation spilling over from Tijuana.

“We didn’t even take our fish finder that day,” Garcia said last week. “I remember the days when I could see the bottom of the riverbed and fish jumping out of the water. I even saw a sea lion one time. In recent years, the water just started to become more turbid.”

But then, something unexpected happened. They found an opaleye inside one of the traps.

That was an exciting moment for researchers at the Tijuana River National Estuarine Research Reserve who have been monitoring the estuary’s health for years and are part of multi-agency efforts to restore the coastal wetland.

“Opaleyes are more marine fish,” said Crooks. “So, this is showing that the species is coming in and using it as a nursery.”

There’s a connection, he added, between the small fish’s presence and the Reserve’s new preliminary findings about alarming dissolved oxygen levels in the water.

Dissolved oxygen is the amount of oxygen present in water. The higher it is, the better the water quality and the more oxygen available for fish and other aquatic organisms.

According to measurements from 2009 to 2023, the number of times low dissolved oxygen levels were detected significantly spiked in 2022 and peaked in 2023. Researchers have observed long periods of hypoxia, in which oxygen levels are severely low (less than 2-3 milligrams of oxygen per liter of water), or anoxia, meaning no oxygen or less than 0.2 mg/L.

“We’ve been monitoring dissolved oxygen in the water continuously since like 1996 so we have a good sense of what oxygen should look like there,” said Crooks. “But what we’re seeing is two or three days in a row of zero oxygen at some of these sites.”

What’s causing this: increases in sewage flows. Last year, the amount of wastewater in the river exceeded 44 billion gallons, the most on record in the last quarter-century.

“Sewage is organic matter and it needs oxygen,” said Crooks. “And when there’s way too much organic matter, the oxygen demand in the water is incredibly high.”

The sewage, he added, is also serving as a fertilizer for plants and they’re absorbing available oxygen, further slowing down water flow.

“Part of what’s happening is that the plants are doing very well,” said Crooks. “The marsh vegetation looks pretty good, right? I mean, sewage is fertilizer.”

The only other time researchers saw low oxygen levels in recent times was during the 2016 El Niño event, which kept the ocean and freshwater from their normal tidal circulation. This blocked the river mouth with sand and created a stagnant pool that killed wildlife, including dozens of leopard sharks.

Researchers at the Reserve also detected long periods of hypoxia conditions this year.

During one week in August, when the total volume of sewage-contaminated water in the river was 304 million gallons, one of their data logging stations measured hypoxia conditions for most of the week, “which is very detrimental to marine life,” said Crooks.

And it is unhealthy for humans, too, said Rachel Smith, a marine scientist at UC Santa Barbara’s Marine Science Institute.

Researchers at the institute were using the Tijuana River estuary as a model for restoring the San Dieguito Lagoon in Del Mar. The restoration project is part of a long-term effort to compensate for marine life lost due to operation of the now-shuttered San Onofre Nuclear Generating Station, according to the institute’s website.

But this year, with pollution and sewage odors at their worst, researchers decided to swap the Tijuana Estuary with Los Peñasquitos Lagoon as a reference site.

“Our staff, they’re in the estuary up to their chest in the water and also the mud,” said Smith. “Over the last two years, we’ve noticed that, in terms of the sewage, it’s gotten a lot stinkier and just a lot more. We were a lot more worried about the safety of our staff.”

Smith said the hope is to return to the Tijuana River estuary in the future because it’s a “beautiful area, and it’s also an important reference site for us, because it’s so close by to a lot of our other reference sites.” The estuary is one of the few intact salt marshes remaining. More than 90% of wetlands in Southern California have been lost because of development and other land use changes, according to the state Department of Fish and Wildlife. It has also long been considered a vital breeding, feeding, resting and nesting ground for more than 370 species of birds.

The UCSB institute found that the number of fish per unit area and the number of different fish species at Tijuana Estuary dropped precipitously from 2021 to 2023 compared to three other wetlands in Southern California. For example, fish density dropped from more than 15 per meter squared in 2021 to less than five in 2023, according to a 2023 San Onofre Nuclear Generating Station Mitigation Program report.

Fish, crab, snail and clam populations took a nosedive over the past couple of years, said Crooks. It’s unclear how many species have left the estuary or have died as a result of pollution.

“We do see dead fish but fish can also swim around and some, like clams, don’t move at all, and others they may not be able to reproduce,” he said. “So, I think it’s a combination of things. My guess is toward the river mouth, things are a little better because dilution is the solution.”

There is some good news.

Researchers recorded a slight improvement in dissolved oxygen levels in the water last month, just a few weeks after Mexico fixed PBCILA, a pump that helps divert millions of gallons of polluted water daily from the Tijuana River and sends it to wastewater treatment plants. The average daily sewage flows dropped from about 45 million gallons to about 6 million gallons. Shortly after, South County residents reported a drastic reduction in noxious sewage-related odors that keep them up at night.

During a week in October, when the total volume of sewage-contaminated water in the river was 44 million gallons, hypoxic conditions were seen 26% of the time, compared to 95% of the time during a week in August, with 304 million gallons of polluted water.

“To be clear, 26% of the time is still very concerning, but it does demonstrate a response of the estuary to decreased flows, with the hope that further decreases in flows would improve conditions more,” said Crooks.

Officials on both sides of the U.S.-Mexico border responsible for wastewater infrastructure say they are working with a level of urgency to complete construction projects as soon as possible.

In San Diego, the International Boundary and Water Commission broke ground on a long-awaited project to repair and expand a treatment plant that serves as a backstop for Tijuana. It’s expected to be completed in no less than five years. Mexico expects to finish by the end of this year a major overhaul of a broken plant that has for years dumped untreated wastewater into the Pacific Ocean.

Though several other efforts are needed to plug Tijuana’s leaky system, the two projects should eliminate about 90% of sewage flows reaching South County shorelines.

Additionally, the U.S. Environmental Protection Agency is reviewing a petition sent by San Diego County residents and elected officials asking the federal government to evaluate whether the polluted Tijuana River Valley may be eligible for Superfund designation.

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