The fine is among the largest in the San Joaquin Valley and California over the past several years, say officials at the U.S. Environmental Protection Agency. Though they didn't have specific numbers, officials said fines of nearly $1 million are unusual in California.
Ampersand agreed to the fines for violations that began in 2008 at the Ampersand Chowchilla Biomass in Madera County and Merced Power near El Nido, the EPA said. The biomass plants burn woody waste from farms and cities to create electricity.
Ampersand agreed to reduce ozone-forming oxides of nitrogen and carbon monoxide. Company officials could not be reached for comment.
The large fine reflects the amount of pollution and duration of the violations. The violations took place during 2008, 2009 and 2010.
The San Joaquin Valley Air Pollution Control District discovered the problems.
Biomass plants are considered a cleaner option than open-field agricultural burning, which has been mostly banned in the Valley.
But modern biomass plants must meet strict standards to prevent adding to the air-quality problems, especially in the Valley.
Valley ozone pollution is among the worst in the nation.
Ozone is a corrosive, warm-weather gas that scars the lungs and triggers asthma.
"Today's enforcement actions are a victory for human health," said Jared Blumenfeld, EPA's regional administrator.
Ampersand was fined $328,000 for its Chowchilla plant and $492,000 for the Merced County operation.
The EPA and the district will split the penalty, which is considered a rarity. EPA and local districts don't often work together on enforcement actions.
EPA's share of the money will go to the U.S. Treasury. The Valley air district uses such penalties to fund programs helping residents buy electric lawn mowers or cleaner-burning wood stoves.
Ampersand also was required to pay an extra $15,000 to the Valley air district for separate violations of district rules, including requirements for emissions control plans.
Ampersand bought and refurbished the two biomass plants in 2007 and 2008, federal air officials said.
The operations had been shut down during the 1990s, according to the Valley air district.
Aside from nitrogen oxides and carbon monoxide, the two plants violated limits for sulfur dioxide. The two plants also failed to perform timely testing to measure emissions, EPA said.