Next time you spray Rover or Fluffy for fleas, you may be harming San Francisco Bay.

An insecticide found in commonly used over-the-counter flea treatments like Frontline Plus and Pet Armor appears to be washing down pet owners’ drains and flowing through sewage treatment plants into the bay, new research shows.

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How much has air pollution changed? Check the plumage While the chemical, called Fipronil, is effective in wiping out annoying fleas, it also is entering the bay at levels that can kill aquatic insects that are a key part of the food chain, providing nourishment to fish and birds.

“The big concern is that we are disrupting the ecosystem,” said Rebecca Sutton, a senior scientist with the San Francisco Estuary Institute, a non-profit research group in Richmond.

“By harming the critters at the bottom of the food web, we could be harming birds and fish,” said Sutton, who has a doctorate in environmental chemistry from UC Berkeley. “We’re trying to provide the science to help correct the problem.”

Pet owners are applying the chemicals, through creams or sprays, to their dogs and cats, and then washing those chemicals down the drain when they wash their hands, their pet’s bedding, their own clothes or even their animals in the bathtub, Sutton said. Since the region’s sewage treatment plants aren’t built with filters to screen out Fipronil and other flea chemicals, they can flow untreated into the bay.

Sutton recommended that people with flea and tick problems instead vacuum their homes more often, and give their dogs or cats prescription pills and other oral medications provided by veterinarians to kill the bugs.

“I’ve switched to them with my two cats,” she said. “We all need to have comfortable homes and happy pets. But there are other options.”

Industry officials say more research is needed.

Fipronil is an ingredient in more than 130 different products in California, including chemicals that pest control companies use to kill ants and other insects inside and outside homes and businesses, said Erin Crew, a spokeswoman for Boehringer-Ingelheim, a German company that produces Frontline Plus.

“The cited studies do not identify a direct causal link to pets as a contamination source,” she said, adding: “We remain committed to address issues that threaten the ability of animals to live healthier, happier lives, including the sustainability of the environments in which they live.”

But researchers say the evidence is getting strong.

In a paper published in June, Sutton and other scientists sampled wastewater coming from neighborhoods into eight sewage treatment plants around San Francisco Bay, from San Jose and Palo Alto to Oakland, Martinez and Fairfield. They also took samples of the wastewater after it had been treated and was flowing out to the bay.

In every case, they found levels of Fipronil in treated wastewater at concentrations between 14 and 49 parts per trillion — all above the U.S. Environmental Protection Agency’s “aquatic life benchmark,” of 11 parts per trillion for Fipronil. The benchmark is a standard that estimates how much of a chemical can be found in a stream, river or lake and not harm insects or fish.

Could the Fipronil have come from somewhere other than pets? It’s not legal to use in agriculture in California, Sutton said. When it is sprayed by pest control companies, it washes into streams, where it also has been detected.

“It’s hard to see how outdoor uses would make it into our water pipes,” she said.

A recent study went right to the washed dogs to learn more.

Jennifer Teerlink, a senior environmental scientist at the California Department of Pesticide Regulation, led a study in which she asked volunteers to provide dogs that had been treated with flea and tick chemicals. The dogs were washed in tubs two, seven and 28 days after the chemicals were applied. The scientists collected the water and performed a detailed chemical analysis and found that Fipronil was present in the water after every dog was washed.

“Results confirm a direct pathway of pesticides to municipal wastewater through the use of spot-on products on dogs and subsequent bathing,” concluded the study, which is scheduled to be published in the December issue of Science of the Total Environment, a research journal.

“It helped us understand the chemical does persist and it does wash off,” said Teerlink. “That is a significant finding.”

More studies are underway. Scientists are measuring the levels of the chemicals in bay mud. And whether the chemicals are killing aquatic insects in large numbers also isn’t known yet.

What can be done? It’s probably too expensive to retrofit the hundreds of wastewater treatment plants around California to filter the chemicals, said Tom Mumley, assistant executive officer of the San Francisco Bay Regional Water Quality Control Board, in Oakland.

But the state could work with the manufacturers to change the labels on the pet products, or to see if smaller doses of Fipronil would work, or to investigate whether other chemicals might work instead.

“We’re looking at how we can manage the source,” said Mumley. “It’s the magnitude of use. Are there viable alternatives, or restrictions on uses? It doesn’t take much of these pesticides. They are toxic at parts per billion.”