Gov. Jerry Brown’s signing of a high-speed rail funding bill Wednesday was great news for the San Mateo County Transit District as more than $600 million was pledged to modernize the Caltrain system.

The money will be used to electrify the tracks for a more efficient and sustainable rail system in an overall $1.5 billion project that could be completed by as early as 2019.

But Caltrain lacks a dedicated source of funding and transit officials are looking at some short-term solutions, possibly a regional tax on a 2013 ballot, that would reduce the burden on the three transit districts that support it — SamTrans, the Santa Clara Valley Transportation Authority and the San Francisco Municipal Transportation Agency.

SamTrans, however, has struggled in recent years, needing to use nearly $10 million a year in reserves to pay down debt related to the Bay Area Rapid Transit extension to the San Francisco International Airport — a debt that is not estimated to retire until 2032. It has also reduced its contributions to Caltrain substantially in recent years, causing the other transit agencies to follow and creating a nearly $30 million annual shortfall for the rail agency.

The SamTrans board passed a $154 million operating budget last month that required the use of $10.6 million in reserves to balance the fiscal year 2012-13 budget despite it having an actual $13.9 million operating surplus.

The San Mateo County Transit District is the administrative body for SamTrans bus service, Redi-Wheels paratransit service and the Caltrain commuter rail line.

Barely supported by fares from its riders, the district’s main focus is to keep the bus system running. The lack of revenue caused the district to slash its annual contribution to Caltrain years ago by more than $10 million.

Reserves at SamTrans have dropped to about $46 million now. Last year, the agency indicated the reserve could dry up by 2015.

The agency projected to run out of reserves in 2010 but has instituted fare increases, service reductions and other measures to push it out to the 2015 date, said Gigi Harrington, SamTrans’ deputy chief executive officer for finance.

"This fall, we will update the model when we close the books and see where we are at,” Harrington told the Daily Journal.

The agency’s employees have also picked up a greater contribution of their pension and health care costs, which has helped SamTrans reduce its reliability on its reserve, said SamTrans’ spokesman Mark Simon.

SamTrans’ debt service requirement this year is $24.4 million, with $12.7 million going to pay down the debt related to the BART airport extension.

"We have some obligations that attack the budget,” Simon said about the BART-related debt and its annual contributions to Caltrain.

The agency is only expected to raise about $17.9 million in revenue this year in fares, a modest 11.6 percent of its overall revenue.

Most revenue, $65 million, will come from sales tax revenue while $46.8 million will come from local sources and operating grants.

SamTrans’ contribution to Caltrain this fiscal year will be $14 million, with $5.2 million of it coming from Measure A funds specifically earmarked for Caltrain.

Another $6.7 million of the contribution is from VTA and SF Muni for a payment related to the purchase of the Caltrain right-of-way nearly two decades ago.

Another $2.1 million is coming from one-time only funds, Simon said.

The right-of-way payments and one-time swaps offer temporary budget relief, Simon said, but will go away.

"The math just doesn’t work out,” he said. "We have to find a way to solve the problem.”

The agency was awarded a $4.9 million grant Thursday from the Federal Transit Authority’s Bus and Bus Facilities Initiative to purchase its first fleet of energy-efficient passenger vehicles. The request was made by U.S. Rep. Anna Eshoo, D-Palo Alto earlier this year.

"After 15 years of solid service for community riders, this award will go a long way toward keeping the SamTrans bus system a viable transportation option,” Eshoo said in a prepared statement. "With these new energy efficient buses, we will have a 21st century fleet that reduces harmful greenhouse gas emissions, keeps costs down and helps grow our local economy.”

SamTrans operates 48 bus routes in San Mateo County but just four them handle nearly half of the transit agency’s weekday ridership.

As it develops a long-range service plan for the next five to 15 years, SamTrans is looking at whether it should invest in beefing up the system’s most productive routes along El Camino Real that could cause some lesser-used routes to be either terminated or consolidated.

The agency is also considering whether it should invest in the county’s core market areas of Daly City, South San Francisco, San Mateo, Redwood City and East Palo Alto or to leave the service essentially as it is now.

The agency has held public workshops the past year to gauge which of the scenarios were most favored.

SamTrans has a weekday average ridership of about 45,000 a day but 45 percent of the riders travel on just four routes: the 120, 292, 390 and 391.

Those four routes are the least costly for SamTrans to run while some local routes, such as the 72 in Redwood City, cost the transit agency nearly $15 per rider.

SamTrans only recovers 12 percent of its cost from the fare box and gets most of its support from tax revenue. Adult fares are just $2 but it cost SamTrans much more than that to accommodate the trip.

Bill Silverfarb can be reached by email: silverfarb@smdailyjournal.com or by phone: (650) 344-5200 ext. 106.