Humboldt Bay was listed as one of the most dangerous harbor entrances in California due to the narrow 0.25 miles (0.40 km) wide channel with tidal currents and shifting sandbars plus unpredictable weather with high winds and heavy fog.

[2] The vegetable oil burning light shone from a 53 feet (16 m) tall tower whose keeper lived in a Cape Cod style house at the base.

[2][3] The lighthouse was damaged in 1877 and 1882 by earthquakes and in 1885 by a flood and was abandoned in 1892,[3] when the entire facility, including the Fresnel lens, was relocated to the Table Bluff Light on October 31.

[4] In 1883 Alexander Ballantyne and Albert Henry Payson, working for the United States Lighthouse Board designed a wharf, stone-cutter's shed, mess hall and housing adjacent to the Humboldt Harbor Lighthouse to prepare and dress hundreds of 2.5 ton granite boulders transported from the Mad River Quarry on railroad flatbed cars transported on barges across the bay.

[5] After the stones were cut precisely to full scale templates with a mortise and tenon such that each would fit only one adjacent block precisely, they were wrapped in rope netting, loaded on a narrow gauge railway by steam-driven crane and moved to the wharf from which they were loaded by another steam crane to specially fitted steamer ships to be taken to form the foundation of the St. George Reef Light, on the site of the fatal Brother Jonathan wreck offshore Crescent City, California.

[5] The original station was to the north side of the present building and tasked to rescue wrecked and stranded ships and patrol the beaches.

[2] In 1936, as part of the national New Deal upgrade of Coast Guard facilities, a new Humboldt Bay Station was built to replace the original.

[2] Two marine railways were built, originally without handrails, from the bay side boat room to seven feet below mean low tide line.

[2] After the Japanese submarine I-17 shelled the SS Emidio offshore Cape Mendocino killing five sailors on December 20, 1941,[6] the station was charged with foot and horse patrols operating along the coast and beaches.

[2] Notable rescues include: The Station received National Register status for significance in helping navigation and saving lives in the area of Humboldt Bay.

[2] Since 1994, the marine railway has displayed Motor Lifeboat #36515, which was decommissioned in 1982, donated to the Humboldt Bay Maritime Museum and returned as a monument.