The Hidden Cost of Flawed Science: How ddPCR Testing is Harming Imperial Beach

By C4CC | April 3, 2026

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A Methodological Crisis Disguised as Progress

In May 2022, San Diego County made a fateful decision that would transform beach management across the region. The county switched from the proven Enterolert culture-based method to a newer technology called droplet digital polymerase chain reaction (ddPCR) for monitoring water quality at coastal beaches. County officials promised faster results and better protection for public health. What they delivered instead was a flawed testing methodology that disproportionately harms the poorest beach community in San Diego while failing to meet federal standards for scientific validity.

Today, nearly four years later, peer-reviewed research confirms what South Bay residents have experienced firsthand: the ddPCR method produces a 56.3% false positive rate, closing beaches that are actually safe and devastating the local economy of Imperial Beach—a working-class community already burdened by cross-border sewage pollution from Tijuana.

This is not a story about better science. It is a story about environmental injustice.

The Science Behind the Problem

To understand what went wrong, we must first understand how these two testing methods work differently.

Enterolert, the culture-based method approved by the EPA and used for decades, measures only viable (living) enterococci bacteria. These are the microorganisms that can actually cause illness in swimmers. The test takes overnight to produce results but provides a reliable indicator of genuine health risk. The EPA established a Beach Action Value (BAV) of 104 colony-forming units (CFU) per 100 mL of water as the threshold for safe recreation.

ddPCR, by contrast, detects DNA—including DNA from dead cells, non-culturable cells, and cell fragments. It produces results in hours rather than overnight, which sounds like an improvement. But this speed comes at a critical cost: the test cannot distinguish between DNA from pathogens that can actually infect you and DNA from pathogens that are already dead and harmless.

As the peer-reviewed study by researchers at San Diego State University and LaRoc Environmental explains, "PCR-based methods can detect free DNA and DNA from dead cells or non-culturable cells, in addition to the DNA from culturable cells, while culture-based methods only detect culturable cells." [1]

The county adopted a new ddPCR-based BAV of 1,413 copies per 100 mL—a threshold derived from a county-wide study that itself showed concerning methodological problems. But here's the critical issue: the EPA has never standardized ddPCR methods for beach monitoring. The EPA's Technical Support Materials state that an alternative method can only be used if it shows consistent agreement with the original method (an Index of Agreement of at least 0.70) or if the correlation is strong enough (R² > 0.60) to develop new numerical limits.

The ddPCR method failed both tests.

The Coronado Study: Evidence of Systematic Failure

In summer 2023, the City of Coronado conducted an independent study comparing ddPCR results collected by the county with simultaneous Enterolert samples collected by the city. The results, published in the Journal of Microbiological Methods, are damning. [1]

The study analyzed 186 water samples collected daily from three Coronado beaches between June and August 2023. Here are the key findings:

What does this mean in practical terms? When ddPCR indicated that a beach was unsafe (exceeding the BAV), it was wrong more than half the time. The Enterolert method—the proven, culture-based standard—showed the water was actually safe. [1]

The researchers concluded: "Overall, the results of this study showed a discordance between the Enterolert and ddPCR methods at Coronado beaches during the summer of 2023, indicating that the relationship may be influenced by spatial and temporal factors." In other words, the two methods don't reliably measure the same thing, and the relationship between them varies unpredictably from place to place and time to time. [1]

The Real-World Impact: Beach Closures and Economic Devastation

These abstract statistical failures translate into concrete harm for Imperial Beach residents.

Before the county switched to ddPCR in May 2022, San Diego County beaches had an exceedance rate of 6.6%—meaning beaches failed water quality tests about 6.6% of the time. After switching to ddPCR, that rate skyrocketed to 59.2% across all county beaches. [1]

But the impact was not uniform. Coronado beaches, which had historically experienced a 3.6% exceedance rate, saw that rate jump to 60.7% after the switch. [1] For Imperial Beach—the community closest to the Tijuana River and most vulnerable to actual sewage pollution—the consequences were even more severe.

According to reporting by Voice of San Diego, Imperial Beach's shoreline was closed 81% of the month of May 2022 alone. [2] These weren't brief, precautionary closures. They were extended shutdowns that devastated local businesses, canceled summer events, and prevented residents from accessing their own beaches.

Two summer beach events in Coronado, including the California State Games junior lifeguard competition, were canceled over water quality concerns. [2] Families couldn't swim. Surfers couldn't paddle out. Lifeguards couldn't safely perform their jobs.

The irony is bitter: the new testing method was supposed to protect public health by detecting contamination more quickly. Instead, it created a public health crisis of a different kind—by falsely declaring safe beaches unsafe, it prevented people from engaging in healthy recreation and damaged the economic foundation of beach communities.

Environmental Injustice: Why Imperial Beach Bears the Burden

Here's where this story becomes a story about injustice.

Imperial Beach is the poorest beach community in San Diego County. It is a working-class neighborhood where many residents depend on tourism, beach recreation, and water-related businesses for their livelihoods. The community is also disproportionately Latino, with a median household income well below the county average. [3]

For years, Imperial Beach has borne the brunt of cross-border sewage pollution from Tijuana. The Tijuana River, which flows through Mexico and crosses into San Diego County approximately 5 miles upstream from its estuary with the Pacific Ocean, regularly carries untreated sewage from inadequate Mexican infrastructure into U.S. waters. [1] Imperial Beach residents have fought for decades to address this problem, filing lawsuits, lobbying Congress, and demanding accountability from federal and county officials.

Then, in May 2022, the county implemented a new testing method without adequate community consultation. According to Imperial Beach Mayor Serge Dedina, the county "blindsided" the community: "In nine years, I had not ever heard back from the county at all on any sort of update on the rapid testing. The next thing you know, there's word the testing has happened, the beaches closed and with any attempt to communicate with the county, the door shuts." [2]

The result? Imperial Beach—already struggling with actual sewage pollution—was now also struggling with false positives that closed beaches based on flawed science rather than genuine health risk. The community that had fought hardest for better water quality monitoring found itself punished by that very monitoring system.

This is environmental injustice: a decision made by county officials, without meaningful community input, that disproportionately harms the most vulnerable community. It is a decision that prioritizes the appearance of rapid action over the reality of sound science. And it is a decision that falls heaviest on those least able to bear it.

The Methodological Failures: Why ddPCR Doesn't Work for Beach Monitoring

Beyond the statistical evidence, there are fundamental scientific reasons why ddPCR is unsuitable for beach water quality monitoring.

First, ddPCR detects DNA, not viable pathogens. The whole point of monitoring beach water quality is to protect swimmers from infection. Viable, living pathogens cause infection. Dead DNA does not. Yet ddPCR cannot distinguish between the two. A beach might test positive for high levels of enterococci DNA while containing no living pathogens capable of causing illness. [1]

Second, the relationship between ddPCR and Enterolert varies by location and time. The Coronado study found that "the empirical relationship between Enterolert- and PCR-based measurements of enterococci in environmental samples is not universal, even at a single beach, due to high temporal and spatial variability." [1] This means you cannot simply convert ddPCR results to Enterolert equivalents using a single formula. The conversion factor changes depending on where and when you're testing. This makes it impossible to establish a reliable, uniform standard for beach closures.

Third, the EPA has not standardized ddPCR methods for beach monitoring. The EPA has standardized qPCR methods (Methods 1611 and 1611.1), but not ddPCR. The EPA's Technical Support Materials explicitly state that only approved EPA methods can be used to support recreational water quality criteria. [1] San Diego County received a pilot program waiver in 2020, but that waiver does not change the fundamental fact that ddPCR has not been validated as equivalent to the culture-based standard.

Fourth, the county implemented ddPCR without proper validation. The peer-reviewed literature shows that the relationship between culture-based and PCR-based methods is complex and varies by location. The county should have conducted extensive validation studies before switching methods. Instead, it appears to have rushed the implementation, leading to the methodological failures documented in the Coronado study.

The Political Dimension: A Decision Made Without Community Input

The scientific failures are compounded by a political failure: the decision to switch testing methods was made without adequate community consultation.

Serge Dedina, the mayor of Imperial Beach and a vocal advocate for addressing cross-border sewage pollution, was not consulted before the switch. When he and Coronado Mayor Richard Bailey sent a letter to the San Diego County Board of Supervisors in July 2022 asking the county to revert to the Enterolert method, they were rebuffed. Supervisor Nora Vargas responded by suggesting that if the mayors wanted to change the testing method, they should "directly petition for a change to the old testing method at the state level." [2]

This response is telling. Rather than engage with legitimate scientific and community concerns, the county official essentially told the elected representatives of the affected communities to take their complaints elsewhere. It is a response that prioritizes institutional inertia over community welfare.

Dedina has speculated that the county's dismissive response is connected to a separate political dispute. In 2021, Dedina co-signed a letter criticizing the county's COVID-19 vaccine rollout program for failing to adequately serve communities of color. After that letter, Dedina says Supervisor Vargas refused to meet with him. [2] Whether or not that political tension influenced the county's response to the ddPCR concerns, the pattern is clear: the community most affected by the decision was excluded from the decision-making process.

The Compromise That Isn't

After the initial beach closures sparked public outrage, the county implemented a compromise: warning signs at beaches that fail the new water quality test, rather than formal closures. This technically leaves beaches open and puts the decision of whether to enter the water up to individual swimmers.

But this "compromise" creates its own problems. Lifeguards are now in an impossible position. Under the old system, when beaches were formally closed, lifeguards could prevent people from entering the water and could refuse to perform water rescues if necessary. Under the new system, with only warning signs in place, lifeguards are expected to enter contaminated water to perform rescues—exposing themselves to genuine health risks based on testing that may be giving false positives. [2]

Moreover, the warning signs place an unfair burden on swimmers. As one Coronado resident pointed out, "What happens if we rely on the old test which is less reliable and timely, now it's left for the public to decide whether we should go in the water, but we can't make an informed decision." [2] Swimmers should not have to become epidemiologists to decide whether it's safe to swim at a public beach.

What Should Be Done

The evidence is clear: San Diego County should revert to the Enterolert culture-based method for routine beach monitoring, at least until ddPCR methods have been properly validated and standardized by the EPA.

This is not a call to abandon better science. If ddPCR can be properly validated and shown to reliably predict health risk, then it should be adopted. But that validation work has not been done. The Coronado study shows that the current implementation fails basic scientific standards for equivalence.

In the meantime, the county should:

1. Revert to Enterolert for routine beach monitoring while continuing to collect ddPCR data for research purposes.

2. Conduct proper validation studies comparing ddPCR and Enterolert across multiple beaches, seasons, and conditions before considering any future switch.

3. Engage with community stakeholders before making decisions that affect public health and local economies. Imperial Beach residents deserve a seat at the table.

4. Prioritize accuracy over speed. An overnight result that is reliable is better than a rapid result that is wrong more than half the time.

5. Address the actual source of the problem. The root cause of beach contamination in Imperial Beach is cross-border sewage pollution from Tijuana. That is the problem that needs to be solved. Better testing methods are useful, but they are not a substitute for actually fixing the sewage infrastructure.

Conclusion: Science, Justice, and the Beaches We Deserve

The story of ddPCR testing in San Diego is a story about what happens when institutions prioritize the appearance of progress over the reality of sound science. It is a story about what happens when communities are excluded from decisions that affect their lives. And it is a story about environmental injustice—how flawed policies fall heaviest on those least able to bear them.

Imperial Beach residents did not ask for a new testing method. They asked for clean beaches and for the county to address the sewage pollution that has plagued their community for decades. Instead, they got a testing method that produces false positives 56% of the time, closes their beaches based on flawed science, and devastates their local economy.

The peer-reviewed research is clear. The community concerns are legitimate. The path forward is obvious: revert to proven methods, conduct proper validation, and engage with communities before making decisions that affect their lives.

Our beaches deserve better. Our communities deserve better. And our science deserves better than this.

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References

[1] Verbyla, M.E., & Lacarra, R. (2026). The relationship between Enterolert and ddPCR concentrations of enterococci in summer samples from beaches in Coronado, California. Journal of Microbiological Methods, 240, 107346. https://doi.org/10.1016/j.mimet.2025.107346

[2] Elmer, M. (2022, July 29). South Bay Mayors Want County to Ditch New Coastal Water Quality Test. Voice of San Diego. https://voiceofsandiego.org/2022/07/29/south-bay-mayors-want-county-to-ditch-new-coastal-water-quality-test/

[3] U.S. Census Bureau. (2020). American Community Survey 5-Year Estimates. Data for Imperial Beach, California.