Today we’ll unpack the science behind a brand-new technology to measure water quality. San Diego is first in the world to use it, and it’s already sparked controversy.

The more sensitive test shows there’s more poo plaguing San Diego’s southernmost beaches than we could ever tell before — especially in summer when coastal cities like Coronado virtually never failed water quality tests using the old tests. In the case of South Bay, there is an obvious source of human sewage that’s plagued the coastline for decades: Tijuana. 

But instead of closing beaches that fail these sensitive water quality tests, the county backed down, replacing closure signs with new ones warning of potential sewage contamination and leaving the decision of whether or not to enter the water up to the public. 

Richard Bailey, the mayor of Coronado, took that to mean the county doesn’t believe what its new test is telling them. He requested data from the county during a slew of Coronado beach closures beginning May 5 to compare results under both the old and new way to test the water. He pointed to examples where the new test showed the water was dirty but at the same time the old test showed the water was safe.

“If the test thresholds are exceeded for the new test…but they are well below the thresholds for the old test, Coronado’s position is that the beaches should be open,” Bailey said.

Scientists say: That’s missing the point.

Here’s why.

How the County’s New Water Quality Test Works

San Diego County worked with the U.S. Environmental Protection Agency, California Department of Public Health and the Southern California Coastal Water Research Project worked for years the testing technology. 

The test, called digital droplet polymerase chain reaction or ddPCR, counts the presence of bacteria in water by its DNA. The old method, called culturing, counted bacteria organism-by-organism under a method that is much less precise.

To count bacteria under the culturing method, scientists have to encourage the gut bacteria to grow so collections of organisms were visible enough to be counted. That process can take up to three days, which doesn’t really help beachgoers, since it tells beachgoers today what the water was like yesterday. Some of that bacteria can die or be unwilling to grow enough to be counted which leads to an inaccurate representation of the water quality.

Both tests – old and new – use the same risk for illness threshold the EPA sets on water quality. If the water quality is so bad that about 30 out of 1,000 swimmers will get sick, then governments should notify the public of that risk, according to those guidelines.

Scientists have to measure something in the water to determine whether it will get people sick. In this case it’s Enterococcus, found in the gut of warm-blooded mammals including humans, meaning it’s shed when mammals poo. Find Enterococcus and there’s a good chance poo is also in the water. Find poo in the water and that indicates a higher chance harmful viruses and pathogens are also in the water. That’s why scientists call Enterococcus an “indicator bacteria.”

The culture-based test, which San Diego had been using for decades, tells us more than 104 Enterococci organisms in a 100 milliliter water sample means the water is too dirty for human contact. 

Once scientists developed the new DNA-counting water quality test, they had to figure out how much Enterococcus DNA also means the water is too dirty for humans. Enter Marva Seifert, an assistant professor at University of California-San Diego who worked on the study behind the new test.

After running hundreds of water samples under both tests, the team of researchers concluded that 1,413 copies of that organism’s DNA are equivalent to the risk posed by 104 Enterococci bacteria. So now, San Diego County knows to post its new beach signs warning of potential sewage contamination when water tests show bacteria DNA above that 1,413 number. “This is the first step in identifying what the correlation is between DNA copy numbers and culture results,” Seifert said. “I don’t think it’s a hard and fast number but it’s a really good indicator that there are potentially harmful bacterial viruses in the water.”

What she means is, that’s the best number given the data the researchers had at the time of the study.

The problem remains that once the new technology is applied to the waters in South Bay, it shows bacteria levels wildly higher than the public expected. So, if beaches were closed solely based on water quality tests, which the county maintains is not the case, then shorelines from Tijuana to Coronado could be closed a lot more often – even in the summertime. 

There are some things neither test can do, like distinguish between human or animal feces in water samples. It’s more dangerous for humans to come into contact with human waste as it can more easily transmit viruses. 

And it might be why the County of San Die­go is being careful when it decides whether to close a beach or not.

“(The test) is not an indicator of human sewage. It could be any type of bacteria from animals or humans,” Elise Rothschild, an environmental health specialist at the county Environmental Health Department, told me.

Nevertheless, that’s why South Bay’s coastal water quality is now being considered unsafe for human health more often than we’ve ever seen before.

In Other News

  • Will Congress ever let San Diego spend the $300 million it gave the region to clean up sewage in the Tijuana River? Two Congressional reps try a new route. (Voice of San Diego)
  • East County files for custody over San Diego land, the latest in wastewater wars. (Voice of San Diego)
  • San Diego received over $300 million from California’s state budget to help relocate railroad tracks from the crumbling coastal bluffs in Del Mar. (Union Tribune)
  • Sempra, which owns San Diego Gas and Electric, signed a preliminary agreement with oil and gas giant ConocoPhillips over a big liquified natural gas facility proposed on the Texas Gulf Coast. (Union Tribune)
  • North County’s community energy company adds Vista to its roster. (Union Tribune)
  • State auditor to review SDG&E’s rate increases amid complaints of monthly bills. (Union Tribune)

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  1. A great big thank you to MacKenzie Elmer for her follow-up article explaining the new beach water quality testing procedure in more detail.

  2. “If the test thresholds are exceeded for the new test…but they are well below the thresholds for the old test, Coronado’s position is that the beaches should be open,” Bailey said. Scientists say: That’s missing the point.” The old test attempted to culture live bacteria, while the new test just lookes for their DNA. ” 1,413 copies of that organism’s DNA are equivalent to the risk posed by 104 Enterococci bacteria” I suspect that is the flaw. DNA from bacteria is not necessarily a living bacteriea. While culturing bacteria from a sample insures you’ve got live bacteria in the water if you get a positive test. Remember, the SARS-CoV-2 RNA was found on bathroom surfaces for hours or even days after contamination, but the virus failed to culture because it was “dead”, and COVID-19 was mistakenly thought to be highly trasmissible from surfaces rather than the air. I suspect the same problem is happening in our sea water, we are detecting DNA from dead & dying bacteria. The new DNA test has a much higher probability of a false alarm, while the old bacteria culture test has a higher probability of a miss or at least a delayed detection.

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