Fog was a major problem in the bay and sometimes the light would be obscured by the fog. A cannon was acquired from nearby Benicia Arsenal with a keeper, Sgt. Edward Maloney, to fire the cannon as a fog signal. For 3 Days Maloney fired the cannon , resting for only two hours. A automated clockwork fog bell was installed in 1856.
The Lighthouse was moved in the 1870's from the top of the hill to Land's End - the far end of the point itself, this was due to difficulty of seeing the light from sea. In building the new lighthouse, A tunnel was cut through the rock to allow easier access to the lighthouse. The canon was replaced by a siren as the fog signal,t. 1874, the siren was washed into the sea during a storm. 1877 the new lighthouse was completed. The black lantern room and lens from the original tower were used, and the old tower capped. The new building was a one-story building with three rooms. The central room was built with heavy walls to support the tower. The tower was 33ft high.
1920's, Point Bonita's lamp was switched from a fixed to an occulating lens. An eclipser was installed within the lens which would block out the light at regular intervals.
In the early 1940's a particularly violent storm washed out the narrow path between the lighthouse and the rest of Point Bonita. A wooden causeway was built to bridge the gap. this was replaced by a suspension bridge, which still stands. (At present, park personnel stand at both ends of the ridge to ensure that no more than five people are on the bridge at any given time.)
Compressed air horns had replaced the old fog signals. By 1979, Point Bonita was the last manned lighthouse in California. The light was automated shortly afterwards. The station, is maintained by the Coast Guard. The original second-order Fresnel lens still graces the tower.