Large storage tanks at an Exxon Mobil refinery in Baytown, Texas, were surrounded by rainwater left behind by Harvey in late August.

Chemical plants and refineries in Texas spewed exceptionally high amounts of pollutants while shutting down their vast operations for last month’s Hurricane Harvey, and again when they restarted, government filings show.

Many plants typically shut down when under the threat of a storm or other natural disaster, looking to prevent a wider catastrophe such as explosion. When shutting down or starting up, a process that can take hours or even days, these plants generally “flare out,” or burn off, toxic chemicals in their systems. Newer or upgraded plants often have systems that reduce emissions during flares or capture some of the substances without having to burn them off.

Some plants in southeast Texas shut down their vast systems ahead of the storm, while others were caught with flooding or loss of power and had to shut down suddenly, according to company emissions reports to the state. While plants perform limited shutdowns at various times for maintenance or malfunctions, a natural disaster can force multiple plants in the same area to shut down around the same time, causing a surge in certain cases in emissions from toxic chemicals like benzene.

The Harvey-related startups and shutdowns produced nearly four million pounds of emissions as of Monday, or about 10% of the entire state’s yearly unplanned emissions, according to company estimates to state regulators. That included about 49,000 pounds of the carcinogen benzene and around 80,000 pounds of the carcinogen 1,3-butadiene, according to the estimates. About one million more pounds of chemicals came from other malfunctions during the storm.

Some of the reports were initial estimates and could change.

Some experts and environmental advocates say that with better planning ahead of storms and better operations more generally, companies could curb some toxic polluting during extreme weather. Industry groups counter that emissions during these times usually don’t pose health risks.

The Texas Gulf Coast boasts the country’s biggest collection of oil and chemical producers. Because of its proximity to shale oil and gas, the industry has been rapidly expanding in new multibillion-dollar investments in the region even as it is seeing stronger storms and related threats.

Some residents in neighborhoods near such plants reported strong and sometimes nauseating odors to city and federal reporting hotlines.

Diana Gonzalez, a lifelong resident of the industrial city Galena Park, about 10 miles from downtown Houston, noticed a gaseous smell coming into the living room during the evening of Aug. 27, two days after the storm made landfall. She moved to another part of the house as her sister’s eyes burned.

“We were saying, ‘Do you smell it? Do you smell that?’” she recalled. “We grew up around refineries all our lives. This smell was different.”

Flooding at an Arkema Inc. chemical plant in Texas during Harvey led to a series of explosions that released chemicals into the air and spurred a lawsuit from local first responders.

Following Gulf Coast Hurricanes Katrina and Rita in 2005, government researchers found that 72% of the storm-related events that led to releases of hazardous substances in industrial settings were due to startup or shutdown operations.

The scientists recommended that plants do a better job of planning for such situations.

Some plant operators still appeared to be scrambling when Harvey hit.

“Given the predictions for Harvey, I think many of the facilities there could have shut down earlier and should not have gone through such a hurried shutdown,” said Sam Mannan, who directs the Mary Kay O’Connor Process Safety Center at Texas A&M University.

Mr. Mannan and others said, however, that companies may not have known how bad the situation would be and try not to unnecessarily shut down a facility because such processes have safety risks, and also could crimp the nation’s energy supply.

A Chevron Phillips Chemical Co. plant in Baytown, Texas, estimated a particularly large amount of emissions from the shutdown of its flooded Cedar Bayou plant, including 28,000 pounds of benzene. The final amounts could change.

A Chevron Phillips spokeswoman said the shutdown at the plant began on Aug. 27 as water levels rose.

Hector Rivero, president and CEO of the Texas Chemical Council, which represents 100 facilities along the Texas Gulf Coast, said the vast majority of facilities shut down during the storm. “Their focus is on protecting people, allowing people to get to their homes, making sure plants are safe from an potential impacts,” he said.

The companies likely won’t be fined for the pollution. Many states, including Texas, generally have exempted the enforcement of violating emission limits during malfunctions and unplanned startups or shutdowns.

Two years ago, following lawsuits by environmental groups, the Environmental Protection Agency issued new rules that would end the exemptions. Texas sued the EPA in the U.S. Court of Appeals to overturn the new rules, saying the companies shouldn’t be cited for events out of their control. The case is on hold while the agency reviews a request for reconsideration.

An EPA spokeswoman said the agency is reviewing the rule to “ensure it aligns with the new administration’s policies.”

Scott Pruitt, the EPA administrator, said in an interview that recent events hadn’t altered his basic approach: that he prefers states have more flexibility in enforcing environmental rules.

Eric Wohlschlegel, a spokesman for the American Petroleum Institute, said no changes are needed because the pollution during the storm fell “far below the concern to human health.”

Public-health experts aren’t so sure. They say that some of the potential health effects are unknowable, because from Aug. 25 to Aug. 31, after Harvey made landfall and while plants were shutting down or malfunctioning, Texas suspended its air-testing monitors to protect them.

State officials reported on an agency website that they found the air was mostly safe after testing began again on Sept. 1. Still, on that day, one air monitor in Houston detected ozone levels that were the highest of 2017 in Texas.

—Timothy Puko contributed to this article.

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