HBBO was established in 1982 by C.J. and Carol Ralph.  HBBO headquarters and several long-term study sites are located adjacent to the Lanphere Dunes Unit of the Humboldt Bay National Wildlife Refuge near Arcata, California.  The area is bordered by the Mad River Slough and coastal dune forest.  The variety of habitats, including riparian and pine forest, fields, and estuaries, supports a high diversity of bird species.  Bird populations have been monitored at HBBO continuously since 1982, making it one of the longest-running bird monitoring stations in the nation.  Its coastal location has attracted many vagrants, including eastern warblers, Ruby-throated Hummingbird and Lesser Frigatebird.

In 1996, HBBO provided support for a collaboration between the Redwood Sciences Laboratory (RSL) and Point Reyes Bird Observatory to establish three monitoring stations on Upper Klamath Lake, forming the foundation of the Klamath Bird Observatory.  When KBO was incorporated in 2000, HBBO became a KBO affiliate.  HBBO, KBO, and RSL still share close working partnerships, collaborating on many projects throughout the year.  

HBBO’s education programs provide opportunities for students and members of the public to learn about birds, bird monitoring, and research techniques.  North American Banding Council certified banders and banding trainers operate the HBBO bird banding station, providing high quality data and training to young biologists.  Students from Humboldt State University contribute greatly to HBBO's program, and in turn benefit from high-quality training opportunties.  Several students have completed independent projects or Master’s theses with HBBO.