When the SMART train begins service between north Santa Rosa and San Rafael by year-end, passengers will pay a base fare of $3.50 plus $2 per zone of the transit system.

A fare increase likely will come after about one year of service, the Sonoma-Marin Area Rail Transit District board of directors voted on June 1.

The news comes as the transit system must submit its fare plan to the Metropolitan Transportation Commission by June 15, so Clipper fare card machines at the stations can be programmed in time to start simulated service runs in September.

The initial 43-mile train route runs from the transit station in downtown San Rafael to the industrial parks near Charles M. Schulz–Sonoma County Airport.

Clipper cards are the only form of rider payment that will be accepted. The cards are already used on Santa Rosa CityBus, Sonoma County Transit, Petaluma Transit, and the Golden Gate Transit buses and ferries. Riders who use one of these systems to get to the train will get a discount of 75 cents to $1.50.

Clipper vending machines will be located at SMART train station platforms and at retail locations in the community. Cards are scanned and automatically calculate the cost of the fare, including discounts and transfers.

The Clipper system will cost $2.5 million to install, but the Metropolitan Transportation Commission, which manages Clipper, has committed to picking up $2 million of that.

The board also approved 50 percent discounts for seniors, college students and veterans.

A special pass purchased through an employer, school, social services agency or other institution will also provide riders with a discount. The year-long SMART EcoPass discount will range from 23 percent for less than 50 passes purchased, to 44 percent for 500-plus passes.

Based on surveys and research that indicate about 3,000 riders, these fares are expected generate $3.9 million annually.

The rail service is set to have a significant impact on Marin and Sonoma employers and their employees. About 30 train trips will be scheduled daily, mostly geared toward commuter hours. SMART has been working with other transit operators, like City Bus in Santa Rosa, Petaluma Transit, Marin Transit, and others to coordinate service.

In the last two years, every local transit agency has made a presentation to SMART with regard to coordinating their schedules with the train’s, in some cases altering, or adding service depending on the amount of ridership.

SMART is also working with chambers of commerce in Santa Rosa and Novato, and also Santa Rosa Junior College, about coordinating shuttle options.

SMART also has staff devoted to working with various companies about the possibility of private shuttle service for their employees.