"We understand no one wants to pay higher fares but riders should know this money can only be spent on these identified projects, which will benefit passengers," Trost said in a statement.
The minimum BART fare, which was at $1.75, will rise to $1.85.
The increase is part of an "inflation-based" increase schedule that has been in effect for a decade, and is expected to raise around $325 million over the next six years, Trost said.
BART's last fare increase was in July 2012.
In San Francisco, Muni also is increasing the price of its 1-, 3- and 7-Day Visitor Passports. The price for each went up $1 yesterday.
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