Vessel traffic management systems can be employed for environmental management where vessel activity may be of concern. One such location is in San Francisco Bay where a variety of vessel types transit a highly developed urban estuary. We analyzed vessel presence and speed across space and time using vessel data from the Marine Monitor, a vessel tracking system that integrates data from the Automatic Identification System and a marine-radar sensor linked to a high-definition camera. In doing so, we provide data that can inform collision risk to cetaceans who show an increased presence in the Bay and evaluation of the value in incorporating data from multiple sources when observing vessel traffic. We found that ferries traveled the greatest distance of any vessel type. Ferries and other commercial vessels (e.g., cargo and tanker ships and tug boats) traveled consistently in distinct paths while recreational traffic (e.g., motorized recreational craft and sailing vessels) was more dispersed. Large shipping vessels often traveled at speeds greater than 10 kn when transiting the study area, and ferries traveled at speeds greater than 30 kn. We found that distance traveled and speed varied by season for tugs, motorized recreational and sailing vessels. Distance traveled varied across day and night for cargo ships, tugs, and ferries while speed varied between day and night only for ferries. Between weekdays and weekends, distance traveled varied for cargo ships, ferries, and sailing vessels, while speed varied for ferries, motorized recreational craft, and sailing vessels. Radar-detected vessel traffic accounted for 33.9% of the total track distance observed, highlighting the need to include data from multiple vessel tracking systems to fully assess and manage vessel traffic in a densely populated urban estuary.