The islands are believed to be about two million years old. There are actually ancient corals that extend well inland, in an area previously comprising the seabed of an ancient sea. The lowering of the sea level have exposed them to the surface. The peculiar "mushroom-like" shapes of some of the islands were caused by the eroding action of the ocean waves.
The national park was created by Presidential Proclamation No. 667, covering an area of 16.76 square kilometres (6.47 sq mi) and signed by President Manuel L. Quezon on January 18, 1940, for the benefit and enjoyment of the people of the Philippines and known as the Hundred Islands National Park (HINP). The Republic Act No. 3655 signed on June 22, 1962, created the Hundred Islands Conservation and Development Authority (HICDA), for the conservation, development and management of HINP. The park including Lucap Bay was transferred from HICDA to the Philippine Tourism Authority (PTA) by virtue of Section 35 of Presidential Decree No. 564.
On April 27, 1982 under Proclamation No. 2183, the national park including Lucap Bay and its foreshore areas, beginning from Sitio Telbang to the east to Sitio Recudo to the west, were declared as a Tourist Zone and Marine Reserve under the control and administration of the PTA. Subsequently under the Presidential Proclamation No. 2237 enacted on November 6, 1982, the parcels of land reserve for the Marine Fisheries Multi-Purpose Farm (created under Proclamation No. 1282 of June 21, 1974) were withdrawn and were also placed under the control and supervision of the Tourism Authority for development purposes.
The Executive Order No. 436 signed by President Gloria Macapagal-Arroyo on June 21, 2005 transferred the administration, management, maintenance, and operation of the whole Hundred Islands National Park (HINP), including all the activities, facilities, and improvements thereafter, from the Philippine Tourism Authority (PTA) to the city government of Alaminos, Pangasinan in pursuit of Republic Act No. 7160, otherwise known as the Local Government Code of 1991, which encouraged the transfer of power and authority from the national government to local government units, in line with the government’s devolution program mandated by the Constitution.
The Cabarruyan Island, the largest island in the island-municipality of Anda, Pangasinan located northwest of the National Park, is often referred to as the "mother island" of the Hundred Islands.
The Sagip Lingayen Gulf Project is a study done in 2010, implemented by the Marine Environment and Resources Foundation Inc. and funded by the Dutch government, in response to the lack of resources on the terrestrial wildlife of the islands. The study assessed and created an inventory of the flora and fauna of the islands to help the city government create an environmental monitoring program to protect the island's biodiversity. Some of the wildlife found living in the National Park are:
Lucap or Alaminos Wharf, the entrance to the National Park, is about 240 kilometres (150 mi) north from the Kilometer Zero marker in Rizal Park in Manila or about 3.75 hours drive by private vehicle. By public transportation from Manila, the bus ride takes about 5 to 6 hours.