In 1827 the French explorer Jules Dumont d'Urville named the bay after Alexander von Humboldt, after noticing it during his first voyage with an astrolabe.

The Dutch Etna expedition of 1858 under Hugo van der Goes was the first to explore and map the bay.

However, it took until March 1910, prodded by German claims on the northern coast of New Guinea, before the Dutch established a city on the bay, Hollandia.

During World War II, the area was occupied by the Japanese in April 1942, was liberated by U.S. forces on April 22, 1944, and became home to a massive U.S. naval base, Naval Base Hollandia.

The base served as General Douglas MacArthur's headquarters until the conquest of the Philippines in March 1945.