The northern elephant seal was hunted to the brink of extinction in a surge of commercial exploitation in the late 1800s. Estimates are that as few as 20 animals survived the period of commercial harvesting. Fortunately, for the species, their pelagic nature and the fact that most seals spend 80% or more of their lives at sea, and that they all do all not return to their rookeries at the same time, ensured that enough seals were at sea to support continuation of the species when sealers undertook wholesale slaughters at rookery sites. Following a slow recovery in the early 1900s, northern elephant seals began to recolonize formerly used sites throughout the 1980s.

Incidental take in a variety of coastal net fisheries does occur, but at low levels. This is assumed to be because northern elephant seals move offshore rapidly after leaving colonies to minimize their risk of shark predation. Most of the prey of the northern elephant seal is either of low commercial value or minimally harvested in fisheries. If the population continues to expand there will likely be new rookeries on mainland beaches, and there will be additional challenges to keep conflicts with humans and domestic and feral animals to a minimum. The risk of transfer of diseases, such as morbillivirus from domestic animals to northern elephant seals, is unknown, but the species is considered to be one of several pinnipeds at high risk of disease outbreaks because of their rapidly expanding population and environmental changes associated with global warming (Lavigne and Schmitz 1990). Tourism at several mainland locations in the United States is extremely popular but highly regulated and is not considered a major threat to the species. Tourist access to nearly all of the islands occupied by elephant seals is controlled by law or otherwise regulated in the United States and Mexico, although a number of Mexican islands are inhabited either year round or most of the year by fishermen and their families.

As the species has now recovered from a very small number of survivors, it has likely lost a considerable amount of diversity from passing through this genetic bottleneck, and may now be at greater risk from disease outbreaks and environmental change.