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The ebbs and flows of researching the Kern River

CSUB biologist Dr. Rae McNeish studies an ever-changing subject

By California State University, Bakersfield

October 31^st, 2025

The first time that freshwater ecologist Dr. Rae McNeish saw the Kern River, she didn’t think there was much particularly noteworthy about it. It was the fall of 2017, and she was in the area for her on-campus interview before joining the biology faculty at California State University, Bakersfield.

Still, with her research focusing on rivers and lakes, she was naturally intrigued by the Kern River and interested in the research possibilities it could offer. She’d be coming to Bakersfield from the Northeast, where she previously studied rivers around Lake Michigan, and would need to find a way to continue her work in the Central Valley.

The unusually high water levels of the Kern River during that first visit might have left Dr. McNeish thinking it was just like any other river, but she would soon discover that was not the case. As she returned to various sites along the 164-mile river during her first couple of years at CSUB, she was struck by how different it looked every single time.

“That was really the first time that I became aware of how dynamic the water flow was in the river,” Dr. McNeish said of one early visit. “I was like, ‘Whoa, the Kern River looks not like a river right now. What's happening? Sometimes it does and sometimes it doesn’t.’”

The mystery of the Kern River is something Dr. McNeish has spent the last several years slowly uncovering, learning about the geology of the river, the politics that surround its water flow, the trash that litters it and the creatures that make it their home. Along the way, she’s put her lab on the map as a leader in Kern River research.

Dr. McNeish’s work has already earned the respect of journalist Lois Henry, who covers water issues in the San Joaquin Valley for her independent, nonprofit news organization, SJV Water. Studying the Kern River in whatever wet or dry state it’s in is something she hasn’t seen anyone else tackle.

“I don’t think anyone has done that kind of exacting research on the river so far,” Henry said. “It’s not political or being done under any agenda. She’s just gathering and analyzing the facts as nature presents them. I think that’s highly valuable to the future of Kern River management.”

As dynamic as the Kern River is, so too has been the process of studying it.

A crash course in the Kern River

Before coming to CSUB, Dr. McNeish studied how humans impact rivers and streams and how changes in the terrestrial environment impact the health and functions of freshwater systems. The volume of trash in the Kern River she noticed from the start would give her plenty to work with to continue that line of research, but she also wanted to learn more about the Kern River overall.

Connecting with Dr. Bob Crewdson — a colleague in the Geology Department in CSUB’s College of Natural Sciences, Mathematics and Engineering — Dr. McNeish got a crash course on the Kern River’s flow. Scouting out field sites suggested by Dr. Crewdson in October 2019, Dr. McNeish was shocked by what she saw.

“There was no flowing water,” she said. “I had never in my life hiked a river that was dry. Usually, the rivers I sampled had a variety of different bottom substrate … there are stones and boulders and sediment and silt. But this (the Kern River) was like walking on a sandy beach.”

The site, right under Mohawk Bridge, was perfect for Dr. McNeish’s litter study, which she was working on with a graduate student named Amy Fetters. They just needed some water flowing, which they got not long after, when Dr. McNeish assumes there must have been a dam release approved by the Kern River watermaster, which manages water resources in accordance with water rights.

“It was just wild how, over the span of a couple of weeks, you went from a very dry riverbed to meaningful, flowing water at Mohawk Bridge,” she said.

Unfortunately, work on the trash study had to be paused during the COVID-19 pandemic. Because of the danger posed by field work near the river, Dr. McNeish always requires her students to work in teams, and social distancing made that impossible.

When it was safe to do so again, Dr. McNeish and the students in her lab resumed their work. Keeping an eye on water levels at her sites, Dr. McNeish sometimes takes students in her classes to the river too.

“My students often have this misconception that it is normal for the river to be dry,” she said. “From my understanding, the river is historically a perennial river, which means it's supposed to have water flowing in it year-round, barring extreme drought conditions.”

California’s Central Valley has historically been a very water-rich area. By the 1860s and ‘70s, settlers were draining ephemeral swamps and damming and diverting water off the river to farm.

This time period kicks off some of the first water rights conflicts, with the decision from an 1888 lawsuit between settlers Henry Miller and James Ben Ali Haggin still in place today. Lois Henry explained that water ownership is shared mostly between a combination of five local agricultural water districts, which gets about 80% of the river. The City of Bakersfield receives the remaining 20% and also controls the riverbed, banks and most of its infrastructure from about Hart Park to Enos Lane.

Water levels in the river at any given time are affected not only by drought conditions, but also by who gets the water when, where it goes and how it’s used. It’s a complicated topic Henry has spent years covering for SJV Water and The Bakersfield Californian, including the ongoing fight between managing agencies and groups like Bring Back the Kern, the Sierra Club, the Center for Biological Diversity and Water Audit California.

For her part, Dr. McNeish strives to remain neutral.

“I’m willing to cooperate and make my data publicly available,” she said. “I’m trying to maintain my scientific independence, but, of course, as scientists, if there are cries for concerns in the environment, we should also be focusing our time and energy on that.”

The ebbs and flows of researching the Kern River

Surveying the river

Working at sites along the Kern River like the Mohawk Bridge, Park at River Walk, Hart Park and the Audubon Bakersfield Environmental Studies Area (BESA) just north of the CSUB campus, Dr. McNeish and her students are now surveying the water quality and wildlife present along the river.

The team will take water samples — when there is water to sample, that is — to measure nitrogen and phosphorus. They observe whether birds are nearby and what kind. Naturally, there are more birds present when water is flowing. They also monitor fish and aquatic macroinvertebrates, like insects, worms, clams, snails and crayfish.

“Macroinvertebrates are a very powerful group of organisms to measure in freshwater systems because they are honest signals of the health and ecological function of your freshwater streams and rivers,” Dr. McNeish explained.

“Some are very sensitive to pollution and some are resistant,” she continued. “If your macroinvertebrate community is dominated by sensitive taxa species, this might be pretty good water quality. But if your community is dominated by pollution tolerant ones and there are no sensitive taxa, then this is a warning.”

That warning could portend nutrient pollution, thermal temperature pollution, excess sedimentation or chemical pollution.

Using tools like a multi-parameter sensor probe, the McNeish team can measure pH levels, salinity, oxygen, conductivity and temperature of the water.

Fish species that the team has seen include crappies, bass and sunfish. They’ve even spotted rainbow trout, which is surprising, given that species typically resides in colder waters; the warmer water of the Kern would be “like sitting in a hot tub,” Dr. McNeish noted.

“At the BESA, we found some unbelievably deep parts of the river, and the deeper the water is, the cooler the water will be too,” she explained. “There's a giant willow overarching into the stream above a deep pool that creates a lot of shade.”

Dr. McNeish noted that there is some mystery as to the origins of the rainbow trout, which have also been spotted by fisherfolk she has talked to in the field. It’s possible the energetic current of the river carried them south from cooler spots upstream, or they could have been planted by the California Department of Fish and Wildlife.

Another way her team can assess what fish are in the Kern River is through environmental DNA, or eDNA, sampling. Collecting water from the river, filtering it and then concentrating and sequencing the DNA gives an idea of the fish present in the water. Because it picks up more dominant DNA and misses fainter traces, the testing isn’t perfect, but it does provide an interesting look into the fish population.

“The eDNA fish taxa list aligned beautifully with our field observations,” said Dr. McNeish, adding that the results revealed some fish her team hadn’t yet seen, like threadfin shad, and confirmed others they couldn’t quite identify confidently, like sculpin.

Surveying fish took a dramatic turn last August, when water was cut off to the Kern River, diverted for riverbed work and agriculture. The major dewatering event led to a mass fish die-off, sparking some urgent discussions on water management and, for Dr. McNeish’s team, a new line of research as their live fish survey became a dead fish survey. For more on this, see When the water disappeared sidebar below.

Research as dynamic as the river

As Dr. McNeish has discovered, the Kern River does indeed offer many possibilities for research, much more than she could ever handle on her own while balancing the courses she teaches.

“It’s hard to conduct research with the faculty member being the spearhead of all the projects,” she said. “We just don’t have time. This is where collaborating with students really helps get these projects off the ground.”

Currently, Dr. McNeish has three graduate students and 11 active undergraduate students working in her lab. One of them, Andrew Alba, recently earned his bachelor’s degree in biology from CSUB and returned this fall to earn his master’s degree and continue his work in the McNeish lab.

Alba, a 32-year-old U.S. Air Force veteran, first got involved in Dr. McNeish’s research as a student in NSME’s Summer Undergraduate Research Experience. Identifying macroinvertebrates, processing leaf samples and testing water nutrients and quality during the month-long program eventually led to Alba becoming a lead researcher in McNeish’s lab as an undergrad, studying how the invasive Tree of Heaven species interacted with the freshwater macroinvertebrate community.

Since last summer’s dewatering and mass fish die-off, Alba has been monitoring the river by taking physiochemical samples and depth measurements, noting wildlife that have been present throughout the dewatering process, observing plant growth and talking with local unhoused people, fishermen and others to see how they have been affected.

Dr. McNeish’s passion for the topic is what inspired Alba to return to her lab and earn his graduate degree under her mentorship.

“Rae is an awesome mentor and really pushes me to do my absolute best,” Alba said. “She is also very personable and understands my family and work duties. I have done more than a few research presentations and half a dozen poster presentations outside of school for her and with her.”

Andrew Alba recently earned his bachelor’s degree in biology from CSUB and returned this fall to earn his master’s degree and continue his work in the McNeish lab. (Photo courtesy of Alba)

Undergraduate student Dana Garcia has been studying microplastics, specifically looking into litter dynamics in the Kern River linked with water availability in the river. Another undergrad, Stephaniee Florez, has been sorting through hundreds of photos of the dead fish from last summer using a computer program and a ruler in each photo to measure the length of each one.

The dynamics of the Kern River have made it a difficult system to study reliably, Dr. McNeish said, but her team is making the most of it. As the water levels have changed dramatically over the last few years, each cycle presents a new opportunity for research.

“We have preliminary data of what the river was like when it was flowing,” she said. “We have been documenting what’s been happening this whole time it’s been de-watered. And then water should eventually return back to the river. So, how’s the river going to change? How’s the wildlife going to change? … Where there’s water, life always comes.”

The health of the Kern River is important not only to the creatures who inhabit it but to the surrounding human community as well. The river represents different things to different people, Dr. McNeish explained. For some, it represents water needed to support their livelihoods. For others, a place to enjoy nature and outdoor recreation.

Dr. McNeish stressed the importance of balancing the use of freshwater resources so they are managed appropriately for current and future needs without sacrificing ecological integrity.

“Water tends to be the lifeblood of human civilization,” she said. “It’s so important to support the human enterprise — economically, culturally, spiritually. If you can’t maintain the ecological integrity of these systems, you’re degrading them in a way that they can’t support the connections we have with them. Eventually those connections just break and sometimes can never be recovered.”

CSUB biology students fan out in the Kern River on Saturday, Aug. 31, 2024, looking for aquatic life. (Photo courtesy of Lois Henry / SJV Water)

A dry river shows the rocks and shells that make up the Kern River riverbed.

Dr. McNeish's research team measures the size of dead fish in the dry Kern River.

Jade Dominguez and Rosario Tapia wade in a portion of the Kern River that still had water on Aug. 31, 2024, documenting aquatic life as part of a river monitoring project. (Photo courtesy of Lois Henry / SJV Water)

When the water disappeared

With the Kern River always changing, the McNeish lab team has had to be flexible. Last August, their plans for a live fish transect survey turned into a dead fish transect survey over the course of a week when flows in the river were cut off.

One day, as the water seemed to be getting lower at some of her research sites, Dr. McNeish found the water at their Bellevue Weir site to be just a minimal flow, with fish crowding in refugia pools — small deeper pockets of the riverbed where water might remain as the river goes dry.

Days later, on Aug. 30, she brought local water journalist Lois Henry along for a story for her organization, SJV Water. They couldn’t have picked a more dramatic day for her to join them, as they were greeted by hundreds of dead fish, most of them still glistening.

“It was as if you just snapped your fingers and the water was gone,” said Dr. McNeish.

At the time, water was still flowing through the BESA, even waist-high at some parts, so when Dr. McNeish heard that the water there was gone too, she couldn’t believe it.

“It was just disappointing, shocking and amazing how it turned from a flowing river into freshwater flats, and so many fish were dead and piled up already,” Dr. McNeish said. “I was like, ‘Oh no! We’ve got to do a dead fish transect survey!’”

With time and water running out, Dr. McNeish enlisted colleagues from the Biology Department and local alumni to help with a survey on Sept. 7, covering one-and-a-half miles of the river in the BESA.

“There were so many dead fish; we literally just could not document them all,” she said. “My preliminary counts are 3,033 dead fish, but there are definitely more than that, because you have literal piles of fish.”

From there, interest in Dr. McNeish’s work grew, landing her team on the front page of the Los Angeles Times.

The fish die-off added fuel to the conflict between water authorities and advocates for returning water to the Kern River. For the latest news on the Kern River, including an ongoing lawsuit brought against the City of Bakersfield by Bring Back the Kern, go to sjvwater.org.

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Footnotes

Story by Kelly Ardis, communications specialist, College of Natural Sciences, Mathematics and Engineering (NSME); photos by Abel Núñez-Guerrero, Outreach & Community College Coordinator for NSME, CSUB file photo and contributed by Lois Henry (SJV Water) and Andrew Alba