SAN FRANCISCO — Voters in two counties north of San Francisco gave overwhelming support in 2008 to a ballot measure taxing themselves to build a new commuter train line.

One problem, though: they haven’t been buying enough stuff.

That means revenue from the 20-year, quarter-cent sales tax approved by voters in Marin and Sonoma counties — clearing a two-thirds supermajority requirement — is falling short of expectations.

And that means plans for the SMART commuter rail line may fall short of voters’ expectations.

“The decline in our sales tax revenue has resulted in a $50 million decline in our debt issuance capacity,” Erin McGrath, chief financial officer for the Sonoma Marin Area Transit District, said in a phone interview last week.

SMART plans to run commuter trains along a 70-mile rail corridor, from Larkspur in Marin County to Cloverdale in Sonoma County, and build a parallel bicycle trail.

The system will be built on an existing railroad right-of-way that shadows the frequently congested U.S. 101 freeway.

Though tracks remain in place on the disused freight-rail corridor, SMART must essentially rebuild the line with new tracks and bridges to support passenger service.

The capital cost for the entire project is estimated at $540 million.

The voter-approved sales tax is the keystone for the system’s capital plan, supplemented by other state and regional sources.

As SMART prepared to bring its proposal to voters in 2008, it released a financing plan, which included what it described as “conservative projections for future tax revenues.”

Those projections were for zero growth from 2008 to 2010, followed by a slow rate of increase, reaching 4% in 2014, when the first trains are supposed to roll.

The trouble is, actual taxable sales in the two counties have been on a negative track.

According to the most complete statistics available from the state’s Board of Equalization, for calendar year 2008, taxable sales in the two-county district were down more than 6% compared to the previous year. The 2008 taxable sales were lower than 2005 levels.

The district has also been forced to adapt to changing bond market conditions, including the meltdown of municipal bond insurers, McGrath said.

The district acknowledged the problem in its most recent strategic plan, issued in June 2009.

With reduced revenue to work with, the SMART board has been put in the position of making Hobson’s choices about how to build its train system.

In a meeting earlier this month, board members, composed of elected officials from the two counties, engaged in public hand-wringing over what portion of the system to build first, raising the specter of conflicts between the two counties over who gets what first.

Officials hope additional federal funds can close the gap.

At this point, SMART doesn’t expect to issue debt before December or January, according to McGrath.

The timing will be dictated by the need to buy trains, she said. Until then, the district can finance its capital needs on a pay-as-you-go basis.

“We don’t want to borrow before we need to,” she said. That is why the district hasn’t done much analysis of the Build America Bond program versus tax-exempt debt.

“That’s just a strategic decision you make when you’re ready to issue, and were not there yet,” McGrath said.

The district is working with financial adviser KNN Public Finance.

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