SAN FRANCISCO >> With construction of commuter train service to Larkspur starting as soon as summer 2017, the transit center in downtown San Rafael will undergo major changes requiring passengers to board buses in new areas.

Officials at the Golden Gate Bridge district, which runs buses in and out of the transit center, are grappling with ways to keep its service running smoothly while accommodating the commuter train.

Squeezing rail and bus service into the site has not been easy to do on paper and will be challenging in reality, a consultant told the Golden Gate Bridge’s Transportation Committee Friday.

“The solution is less than ideal,” said Edgar Torres of Kimley-Horn and Associates, Inc.

It was the Golden Gate district that gave SMART — Sonoma-Marin Area Rail Transit — a right of way through the center, so the disruption is not a surprise. But construction, new tracks, barriers and crossing arms that will be added to the site will change how business is done there.

“With the train coming through the station we lose some platform capacity and it has to go somewhere,” said Ron Downing, director of planning for the Golden Gate district.

The rail line will go through platforms C and D, meaning buses will have to pick up passengers on adjacent streets instead. The Marin Airporter will pick up its passengers on Fourth Street under Highway 101, a block away from the transit center. Cijos Street will also undergo improvements so it can better accommodate bus traffic.

“It’s the best we could do given the street alignments, the traffic conditions and where the buses are coming from,” Downing said. “It’s a very challenging environment around the San Rafael Transit Center.”

The modifications are expected to cost about $3.5 million. Exactly who will pay for the work is being negotiated, officials said.

The transit center — known as the C. Paul Bettini Transit Center for a former mayor — opened in 1991 and is used by 9,000 people daily.

The changes will be permanent even after SMART finishes putting track through the transit center. That’s because the rail line will have to be sectioned off by concrete so pedestrians can’t cross tracks, limiting access to buses at the center. Presently, pedestrians can go from platform to platform without restriction.

The bridge district eventually wants to build a new transit center in the same area, but has not identified a location. A new site will likely involve buying property that currently has buildings. But passengers will have to live with the new alignments for at least five years, officials said.

The first phase of the SMART project, which will run from downtown San Rafael to the Santa Rosa Airport, is set to open later this year at a cost of $428 million. That will not affect the transit center.

But last December SMART officials announced the agency was in line to receive funding to extend the commuter rail service to Larkspur, which would be part of a second phase going through the transit center.

Golden Gate planners thought they would have more time to work on a new transit center, but with the funding to Larkspur now available to SMART, that process has sped up. There is a 2005 agreement among Golden Gate, SMART and others that addresses a new transit center.

“We need to work aggressively with Marin Transit, the city of San Rafael and SMART to come up with an agreement for the permanent solution so that when SMART goes to Larkspur the 9,000 existing bus passengers that use the transit center are not left in the lurch,” said Denis Mulligan, Golden Gate general manager.