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A new passenger train system for Sonoma and Marin counties has begun operation, marking the long-awaited launch — nearly four years behind its original schedule — of a $600 million taxpayer-funded transit option designed to transform travel north of the Golden Gate.

Already one of the largest public works projects of the North Bay in decades, the Sonoma-Marin Area Rail Transit system was built on the premise that thousands of weekday commuters, along with tourists and weekend riders, will prefer to hop aboard diesel-powered trains rather than crowd into traffic on Highway 101.

“They’re on the trains, and they’re looking at the stopped traffic on 101, and they’re totally sold that this is a better way to travel,” predicted Debora Fudge, Windsor’s mayor and chairwoman of SMART’s board of directors.

The SMART system begins accepting its first fully paid riders Sept. 5, the first passenger cars to serve the North Bay after a nearly 60-year absence.

SMART’s advocates bill it as a potential game-changer for the North Bay, touting a vision of a new rail system that frees more commuters from their cars, eases highway congestion, reduces vehicle emissions and lays the groundwork for future residential and commercial development oriented more toward walking or riding a bike.

With 10 stops along an initial 43-mile line from northern Santa Rosa to San Rafael, the development has been fraught with obstacles and delays. Steep financial shortfalls tied mostly to a recession-era drop in the voter-approved sales tax that supports the system forced officials to postpone buildout of the full 70-mile line — from Larkspur to Cloverdale — and the accompanying bike path promised at the ballot box in 2008.

Those shortcomings continue to provide fodder for the system’s critics, who question SMART’s sustainability and the expenditure of taxpayer dollars for a system where the extent of rider demand remains largely a projection at this point.

“They have spent, according to their financial audit reports, over $600 million on this train and they haven’t taken a single (paying) passenger,” said Mike Arnold, a Novato economist who backed an unsuccessful effort to repeal SMART’s sales tax in 2012. “The issue with the train is that it costs a lot of money and it doesn’t generate many benefits because it doesn’t take many riders. It’s been the No. 1 issue from the get-go.”

But for supporters, including transportation planners, environmentalists, employers and untold commuters, the start of service is a triumphant moment.

“We think as we prove to the public that we are dependable, that we are reliable, and (for) those whose origin and destination and schedule matches ours — this is an option they’ve never ever had before,” said Farhad Mansourian, SMART’s general manager since 2011.

Questions remain about whether SMART’s planners have found the right formula for schedules and fares — perhaps the two most important calculations determining the venture’s success.

The schedule calls for 34 trips on weekdays, with 30-minute intervals across most of the peak hours, though some gaps of an hour or more still exist. The average overall fare is $5.25 with discounts factored in. Without discounts, the average fare is $7.50, with a one-way trip from Santa Rosa to San Rafael going for $9.50, and a roundtrip $19.

SMART forecasts a daily weekday ridership of 3,000, a number that has fluctuated over the years. SMART is charging a $3.50 base fare and $2 for each zone line crossed. Discounts will offer lower fares for youth, seniors, veterans, college students and disabled riders, as well as commuters who get their tickets in bulk through employers. Monthly passes sell for $200.

Critics say SMART is not living up to its promised mandate to voters in several key areas, including with the schedule trains are operating on. The schedule includes some 90-minute gaps during hours of peak service. The 2008 sales tax measure promised passenger service would be delivered at 30-minute intervals during “rush hours.” A 2014 strategic plan for the system also stated that trains would be “spread across the morning and evening commute hours with roughly 30-minute headways,” and that trains would travel approximately 30 minutes apart.

SMART now says it lacks the equipment and personnel to uniformly offer service on a 30-minute timetable during peak hours.

Parking for access to the trains is another concern. SMART has 268 parking spaces at three stations: in Rohnert Park, and in Novato near Hamilton Parkway and at Atherton Avenue/San Marin Drive. The rail agency is planning an additional 50 parking spaces each at the downtown Petaluma station and the Airport Boulevard station north of Santa Rosa.

SMART’s advocates say such challenges are to be expected with the launch of any major public transit service.

“People said the same thing about BART when BART started — oh, it’s never going to work, no one is going to ride it. And yet the Bay Area wouldn’t work without BART today,” said Susan Klassen, Sonoma County’s transportation and public works director.