Weddell seals served as an important source of food for men and dogs throughout the early periods of Antarctic exploration. They continued to be taken to feed sled dogs at one base in to the 1980s. Local populations of seals no doubt suffered declines from these harvests, but in the case of the population in McMurdo Sound the population has recovered in the 20 years since the harvest ended. At present, there are no immediate or significant threats to the Weddell seal.

The effects of global climate change on Antarctic seals are unknown. However, Learmonth et al., (2006) suggest that Weddell seal numbers may decline with increasing temperatures if Antarctic sea ice is significantly reduced. Loss of sufficient areas of fast ice habitat used for pupping, resting, avoidance of predators (possible), and access to preferred foraging areas because of changes from warming could lead to population declines of Weddell seals. This is in contrast to a paper by Proffit et al. (2007), which reports that the localized cooling and increased sea ice extent in the Ross sea is associated with decreased reproduction and lower weaning mass of Weddell seals in McMurdo Sound. Thus, the overall effects of global climate change on Weddell seals is unknown.

Two of the four species of Antarctic ice seal, the leopard and crabeater tested positive for antibodies to canine distemper virus (CDV). Weddell seals were tested and did not have any antibodies, and Ross seals were not tested. A mass mortality of crabeater seals occurred in 1955, and many animals displayed viral illness symptoms prior to death (Bengtson and Boveng 1991).

Seasonal tourism in the Antarctic and sub-Antarctic has increased steadily in the last 30 plus years, and is currently at all time high levels. The effects of increased vessel noise, disturbance from vessels passage, and close approach by people in small boats and on land or ice on Weddell seal behaviour, distribution, and foraging are unknown. There is also a risk of injury to a small number of animals from collision with boats or crushing from large vessel passage through and disruption of ice fields. There are no reports of significant fisheries interactions.