For many parts of the Bay Area — which lifted indoor mask mandates in certain settings recently after reaching high vaccination rates and low case rates — the state’s announcement will mean a return to indoor masking in offices, gyms and other places where vaccinated people had been able to go maskless.

The state’s move does not appear to affect indoor dining rules, which will continue allowing patrons to remove masks while eating and drinking.

New York state also recently imposed a sweeping mask mandate that took effect Monday and will remain in place until Jan. 15.

In addition to the tightening mask rules, California will require people attending mega-events of 1,000 people or more that don’t require vaccination to show proof of a negative test taken within one day for an antigen test, and within two days for a PCR test. The previous window was 72 hours.

And it will recommend that travelers arriving in the state get tested three to five days after arrival, regardless of vaccination status.

California has always required unvaccinated people to wear masks indoors, but mask rules for vaccinated people vary by county. In several Bay Area counties, vaccinated people no longer have to wear masks indoors in select settings — such as offices in San Francisco, Contra Costa and Alameda counties where everyone is vaccinated. And Marin County no longer requires residents to wear masks in most public settings because its vaccination rate is so high.

The state indoor masking rule that takes effect Wednesday will override these local exemptions, Bay Area health departments said Monday.

“To align with California’s requirements, San Francisco is suspending its current mask exemption for stable cohorts of 100% vaccinated individuals (which includes certain work settings, gyms, and other select locations) until the state order is lifted, currently set for January 15,” the San Francisco Department of Public Health said in a statement.

After Jan. 15, “California will make further recommendations as needed in response to the pandemic,” the state said Monday.

Some business owners took the news in stride. “I don’t think an extra month is going to cause any extra ruffles,” said Dave Karraker, co-owner of MX3 Fitness in San Francisco and spokesman for the SF Independent Fitness Studio Coalition. “Everybody we work with is focused on health and wellness. These are the folks who are thinking first and foremost about how to stay safe and keep people safe.”

The return of universal indoor masking statewide is meant to avoid a repeat of last winter’s deadly surge, which in California marked the worst period of the pandemic to date. Between late December 2020 and February 2021, 20,000 Californians died from COVID, Ghaly said.

COVID case rates statewide have jumped 47% since Thanksgiving, from 9.6 cases per 100,000 people per day to 14 cases per 100,000 people per day, Ghaly said. And hospitalizations have risen 14%.

“This is a critical time,” Ghaly said. “We have a tool we know has worked and can work. We are proactively putting this tool of universal indoor masking in place to ensure we get through a time of joy and hope without a darker cloud of despair. Californians have done this before, and we believe we can do it again.”

The omicron variant, which has prompted stark warnings and renewed restrictions in Britain, is also clouding officials’ view of the future.

“On June 1, I was optimistic we were heading toward the endgame and unfortunately found that wasn’t the case with delta,” said John Swartzberg, an expert in infectious diseases at the UC Berkeley School of Public Health. “Now we see omicron and it’s hard to guess how many more tricks this virus has up its sleeve.”

Swartzberg said that the data is “very compelling” that omicron is more effective at evading immunity from both the vaccine and prior infection.

Some infectious disease experts said California’s move is overly blunt, and does not take into account the vast differences in vaccination and hospitalization rates across the state. Marin and San Francisco counties, for instance, have vaccination rates at or over 80% and are managing to keep hospitalizations relatively low and stable, while many Central Valley counties are less than 50% vaccinated and are seeing surges in hospitalizations.

“To impose a statewide mask mandate kind of takes away the ability for local county officers to make their own decision based on vaccination and hospitalization rates,” said Dr. Monica Gandhi, an infectious disease specialist at UCSF. “In this case, blunt instruments sort of give you no nuance to this aspect of rewarding the high-vaccination regions. We’re going into winter really well poised here in San Francisco. I think it’s overkill, it’s blunt and will receive pushback in the state of California.”

Chronicle staff writer Aidin Vaziri contributed to this report.