City officials objected to the noise, speed and frequency of the trains as they passed through Novato. The Novato City Council Monday night voted 4-0 in favor of a consent decree that settles the lawsuit, which was filed in September 2007. The agreement was reached Monday.
Marin County Superior Court Judge James Ritchie must ratify the agreement, possibly as soon as Thursday.
The settlement means the North Coast Rail Authority can begin repairing bridges and track bed along the 62-mile stretch of rail between Windsor in Sonoma County and Lombard in Napa County, the NCRA's Cloverdale Chairman Allan Hemphill said.
"This settlement establishes an equitable balance between the region's desire to restore train service and Novato's desire to minimize impacts," Hemphill said in a news release.
Hemphill said the NCRA hopes to complete repairs on the first 62 miles of track within four to six months and begin limited freight service in spring 2009.
Under the agreement, the rail authority will be limited to the operation of six freight trains per week during daylight hours until improvements to reduce noise and promote safety are complete.
The NCRA must install Federal Railroad Administration-certified "Quiet Zones" at 13 locations within Novato where public roads cross the tracks. Improvements to the crossing gates and signage will allow trains to travel through the crossings without sounding train horns.
The NCRA also agreed to install welded rail to further mitigate noise; fencing to discourage trespassing; landscaping to minimize glare from train lights; and purchase state-of-the-art locomotives to reduce greenhouse gas emissions.
The "Quiet Zones", fencing and landscaping within Novato city limits must be completed by Dec. 31, 2011.
Until the mitigations in the agreement have been satisfied, the rail authority cannot operate more than three roundtrips per week. The cost of the mitigation measures is estimated at $1 million. The rail authority also will pay Novato's legal costs of $325,000.
The NCRA plans to release in November its environmental report that evaluates its train operations along 142 miles of track between Willits in Mendocino County and Lombard in Napa County. The report anticipates a maximum of three roundtrips per day by the second year of operation.