Tolls are collected manually or electronically in one direction on each of the state-owned bridges according to a toll schedule established by BATA and the California Legislature. For the typical automobile, a $5 toll is collected — a $1 base toll, $1 for Regional Measure 2 and a $3 seismic retrofit surcharge. The toll schedule for the San Francisco-Oakland Bay Bridge is different during weekdays when congestion pricing is in effect. Multi-axle vehicles pay a higher base toll with the toll determined by the total number of axles on the roadway in a vehicle combination. The complete toll schedule, including future toll increases for multi-axle vehicles, can be found on BATA's website.

In fiscal year 2010-11, approximately 122 million vehicles crossed the seven state-owned toll bridges in the Bay Area, generating approximately $615 million in total toll revenues — including $138 million in base toll revenues, $114 million in Regional Measure 2 revenues and $345 million in seismic retrofit surcharge revenues.