Chris Faust gasped when he opened the July garbage bill for his duplex in Noe Valley, thinking perhaps there had been a mistake.

It had shot up from $42.40 to $61.30 for the month — a 45 percent increase, significantly more than the 14 percent hike many city residents were expecting under a new rate structure.

“My first reaction was, ‘Oh, my gosh!’” said Faust, a middle school science teacher.

The rates, approved by a city board in June, were debated during four months of public hearings. San Francisco’s long-standing waste hauler, Recology, pushed for the increase, saying it would help offset the cost of a five-year labor agreement, a new landfill contract and trucks that had to be redesigned to accommodate a surge in recyclable materials.

After 11 hearings, the Refuse Rate Board — which includes the city administrator, city controller and general manager of the San Francisco Public Utilities Commission — approved a complicated new rate structure recommended by Public Works Director Mohammed Nuru. He and other city officials said it reflected the true cost of getting to zero waste in San Francisco.

But the new rates had two side effects. The increases were much steeper for owners of duplexes, residences with in-law units and other small properties. And counterintuitively, the new rates gave owners of small multiunit buildings an incentive to cut down their recycling and composting.

The big cost driver for small residential buildings — those with up to five units — was a service fee applied to every individual dwelling on the property that tripled from $5 to $15. It meant that buildings with four or five units got hit the hardest. Those buildings also pay $6.26 each for a 16-gallon trash bin, a 32-gallon compost bin and a 64-gallon recycling bin. Different combinations with bigger bins are available at higher costs.

Beth Wells, who owns a condominium unit in Lower Pacific Heights, was flummoxed when the garbage bill for her four-unit building soared from $55 to $98 a month, mostly because of the additional $40 in dwelling unit fees.

The “July bill was 78 percent higher than my June bill,” Wells wrote in a peeved email to Recology’s customer service department. She called the new fees “ludicrous.”

Recology spokesman Robert Reed defended the hike, saying the dwelling unit fees help cover the costs of running a recycling plant, maintaining a fleet of trucks and paying workers, costs that exist no matter how much material the company collects each week. The fees also pay for citywide services like sidewalk trash cans and hazardous-waste drop-offs, Reed said. For every dwelling in a building, there’s a household benefiting from those services, he said.

The city authorized a different rate structure for large apartment buildings, charging them $5 for each dwelling unit and about $24 for each 32-gallon bin, regardless of what it contains. Public Works also lowered the “diversion discounts” it offers these buildings, based on how much they compost and recycle. Most large apartment buildings saw an increase in their bills of 12 to 16 percent overall.

In explaining the new structure to the public, city officials emphasized the effect on the typical owner of a single-family residence. People in that category saw a 14 percent jump in July, from $35 to $40 a month for three 32-gallon bins.

When the rate structure was proposed, 13 people wrote letters of appeal, some pointing out that the increases would be much higher for landlords of small multiunit buildings. One letter writer accused the city of discriminating against small property owners because they represent a minority of customers.

The rate board dismissed those objections when it made its final decision in June. Public Works officials and representatives of Recology said the new rates actually create more parity between small and large apartment buildings in the city: Take a garbage bill, divide it by the number of dwellings, and the average household cost usually falls between $24 and $28 a month for basic service, Reed said.

In previous years, small property owners paid less for their units than other customers, said Nuru, noting that the new distribution “is more equitable.”

But when the new bills first arrived in late July and August, owners of small buildings and tenants who pay their own trash bills were caught by surprise. Although they were warned that the price was going up — the rate increases were published on city websites and in newspapers, presented to neighborhood groups, and outlined in a letter that Recology sent to all of its residential customers — many had anticipated the 14 percent hike.

“I looked (at my bill) and I went, ‘Oh my God, I can’t believe this,’” said Marvin Rous, a retired criminal defense lawyer who owns a Victorian duplex near Dolores Park. His bill climbed 38 percent, from $40 to $55.

Small-building owners voiced their complaints on Facebook and Nextdoor.

Mostly, they were angry about disparities. Because of the dwelling unit fees, an owner of a duplex or in-law unit pays substantially more than an owner of a single-family home for the same garbage service.

That seemed unfair to Margie Wylie, who owns a house with a separate cottage in Bernal Heights.

She pays $67.56 a month for a 32-gallon trash can and two 64-gallon bins for compost and recycling. A single-family home with that configuration would pay $52.56 a month.

“This is another example of the middle class in San Francisco getting the burden,” she said.

And some, like Marilyn Scholze, who owns a building with an in-law unit in Bernal Heights, pointed to an unforeseen problem: The new rates lowered the price for trash pickup at single-family homes and small buildings, while raising the price to recycle bottles and compost kitchen scraps.

As a result, Scholze’s trash bill got chopped in half, but her recycling and composting fees tripled. With the dwelling unit increase, the bill shot up $21 a month overall, from $40.34 to $61.30

“When I called Recology, (they said) the only way they could decrease (the bill) was to decrease my 64-gallon recycling pail to 32 gallons,” Scholze said.

“I rarely use my trash because we recycle so much,” she continued. “I will now fill my recycling and put overflow into trash until this is addressed.”

No one in the city had foreseen that the new rates would discourage residents from recycling. But several officials said that after years of bending over backward to get residents to compost and recycle, Recology had to start charging more for those services.

“When the city (instituted) mandatory composting and recycling (in 2009) ... we created incentives to get businesses and residents to do the right thing,” said Guillermo Rodriguez, spokesman for San Francisco’s Department of the Environment. “But as the black (trash) bin shrinks, the cost of maintaining programs and services is still there,” he noted. “It still costs money to get to zero waste.”

Wylie, in exasperation, changed the configuration of her bins on Tuesday, increasing the trash to 64 gallons and reducing the compost and recycling to 32 gallons each. Her new setup goes against San Francisco’s zero-waste credos, but Wylie said it won’t affect her monthly bill.

“I know I sound like the worst global citizen in the world right now,” she said. “But it’s a lot of trouble to sort through (that waste), and they’re not encouraging me to recycle.”

Rachel Swan is a San Francisco Chronicle staff writer. Email: rswan@sfchronicle.com Twitter: @rachelswan

Recology rates

To see the new Recology prices and a rate calculator, go to: www.recology.com/recology-san-francisco/rates/