It has been the site of at least eight known shipwrecks, including the Japanese Wiji Maru, SS Quartette, and most recently the M/V Casitas, which ran aground on the reef in 2005.

Twenty-two bird species nest and breed on the islands, including twenty percent of the world's population of black-footed albatrosses.

Ghost nets and other fishing debris, rising sea levels, and the invasive algae Chondria tumulosa pose a significant risk to the atoll and its wildlife.

[1] The atoll's land area consists of several small islands which are periodically washed over when winter storms pass, along with several ephemeral sand spits.

[15] 46 of the sailors took passage on the Earl of Morby, but Robinson and eleven others opted to purchase the vessel they had built and sail it back to Honolulu in the hopes of recovering some of the losses incurred by the wreck.

[20] In 1930, the United States Bureau of Fisheries decided to conduct a thorough study of the atoll, led by Dr. Paul Galtsoff.

[19] The United States Navy loaned the minesweeper ship Whippoorwill for the five-week expedition, which covered the reef's geography, flora, and invertebrate and fish populations.

[14][19] The Whippoorwill expedition documented wildlife aside from the oysters: Dr. Galtsoff's report indicated that they had found seals, sharks, sea turtles, albatrosses, booby birds, and numerous species of fish.

[16] On December 21, 1952, the SS Quartette, a 422-foot-long (129 m) Liberty ship weighing 7,198 tons, struck the eastern reef of the atoll at a speed of 10.5 kn (19 km/h; 12 mph).

The ship was driven further onto the reef by rough waves and 35 mph (56 km/h) winds, which collapsed the bow and damaged two forward holds.

[24] On July 2, 2005, the 145 ft (44 m) research vessel M/V Casitas, chartered by the National Oceanic and Atmospheric Administration (NOAA), ran aground on the north end of the atoll.

[25][26] The ship was carrying large quantities of gasoline, diesel fuel, and oil, which posed a substantial risk of leaking.

She was towed to a site northwest of Pearl and Hermes Atoll approved by the Environmental Protection Agency (EPA), where she was sunk in waters over 7,000 ft (2,134 m) deep.

Researchers theorized that the wreckage was an East Asian fishing vessel that struck the reef sometime after 1918, based on the age of the components.

[13] A number of artifacts were found at the Pearl site, including anchors, two cannons, and large try pots for rendering whale blubber.

As an example, Setaria verticillata, an undesirable noxious weed, has displaced the native grass Eragrostis variabilis on Southeast Island.

[5] An illegal landing by the military in the 1960s brought invasive field mustard seeds from Midway Atoll, which had to be removed by the U.S.

Although it provides food and nesting space for small songbirds, it poses a significant threat of entanglement to native seabirds, so removal is considered a priority for conservation purposes.

[30] The Pearl and Hermes Atoll provides an extensive and unique habitat for invertebrates, including various sponges and thirty-three species of stony corals.

[19] The Pearl and Hermes Atoll supports breeding populations of endangered Hawaiian monk seals and sea turtles.

[24] In 2016, scientists from the Bishop Museum, working with the NOAA, described a new species of butterflyfish found off the Pearl and Hermes Atoll, at a depth of 180 ft (55 m).

It was named Prognathodes basabei in honor of diver Pete Basabe, who provided support to the dives that first discovered the species.

The region was first protected in 1909 when U.S. President Theodore Roosevelt created the Hawaiian Islands Bird Reservation through Executive Order 1019, which included Pearl and Hermes Atoll.

[33] Over the next century, protection of the region increased incrementally, culminating in President George W. Bush signing Proclamation 8031 in 2006, designating the waters of the Northwestern Hawaiian Islands a national monument under the 1906 Antiquities Act.

[34] Derelict fishing gear (ghost nets) and other types of marine debris have had a major impact on the reefs and associated fauna of the atoll.

[35] Efforts have been undertaken to lessen the threat of this growing problem, including attempts at prevention as well as recurring debris removal projects.

A multi-agency study was launched in 1999 to remove and catalogue debris from the water surrounding Lisianski Island and Pearl and Hermes Atoll.

[36] During this project, a total of 9.6 short tons (8,676 kg) of debris was removed from reefs and beaches around Pearl and Hermes.

[39] Rising sea level is also a major concern for the atoll due to the extremely low elevation of most of the islands.

[5] Estimates of total land area loss range from 15% to 65% in a scenario of median sea-level rise, threatening the habitats of monk seals, sea turtles, and nesting birds.