There is growing evidence that smaller vessels not required to broadcast data via the Automatic Identification System (AIS) contribute significant noise to urbanized coastal areas. The Marine Monitor (M2), a vessel tracking system that integrates AIS data with data collected via marine radar and high-definition camera, was employed to track all vessel types (regardless of AIS data availability) in a region of San Francisco Bay (SFB) where high-speed ferry, recreational, and commercial shipping traffic are common. Using a co-located hydrophone, source levels (SL) associated with 565 unique vessel passages were calculated and resultant cumulative daily sound exposure levels across the study area were modeled. Despite large ships primarily having the highest SLs, ferries and motorized recreational craft contributed noise to the largest area in two frequency bands of interest. The M2 provided data without the need for an on-site observer and enabled a systematic analysis of all relevant vessel types which showed that non-AIS vessels should not be excluded from consideration, especially in a highly urbanized estuary like SFB. This research provides an assessment of underwater radiated noise from all common vessel types in SFB suitable for informing habitat quality and threat evaluation for local cetacean species.