The harbor village is located in a ravine at the northern tip of the Potrero Hills and alongside a small cove the opens to San Pablo Bay, where the marina is protected from waves, in addition to a breakwater.
The harbor is also the starting point for visitors to East Brother Light Station a historic landmark.
The hills surrounding the village feature Eucalyptus trees and coastal chaparral vegetation.
Other animals in the area include the endangered salt marsh harvest mouse and California clapper rail.
The Point San Pablo Preservation Society is a non-profit organization located at the harbor.