Southern elephant seals were hunted for thousands of years by aboriginal and native peoples in Australia and South America. More recently, they were subjected to intensive commercial harvests starting in the early 19th century and not ending until 1964 at South Georgia. They were prized for their large quantity of blubber that could be rendered to fine, valuable oil.

There are few threats and conflicts today, as southern elephant seals live far from human population centres and have minimal interactions with commercial fisheries. Intensive fishing could potentially deplete important prey stocks. However, relatively little is known about their feeding habits. There is no evidence that recent declines for animals breeding in the Indian and Pacific Oceans are related to fisheries in the Southern Ocean (SCAR 1991). However, development of new fisheries at high latitudes in the future could have a significant impact on elephant seal populations (SCAR 1991, Reijnders et al. 1993).

In the South Orkney Islands a few young male elephant seals were killed for dog food in the 1950s and early 1960s when they were ashore moulting. Southern elephant seals that haul out at mainland sites could come in contact with feral dogs and other terrestrial carnivores and be exposed to a variety of diseases including morbiliviruses.

The possible effects of global climate change on southern elephant seals are not well known. Learmonth et al. (2006) suggest that while the effects of global climate change are uncertain, that the species is likely to decline as a result of habitat and ecosystem changes.