Since 2008, the Baikal seal has been listed as a Least Concern species on the IUCN Red List. This means that they are not currently threatened or endangered. In 1994, the Russian government estimated that they numbered 104,000. In 2000, Greenpeace performed its own count and found an estimated 55,000 to 65,000 seals. The most recent estimates are 80,000-100,000 animals, roughly equaling the carrying capacity of the lake.
In the last century, the kill quota for hunting Baikal seals was raised several times, most notably after the fur industry boomed in the late 1970s and when official counts began indicating more Baikal seals were present than previously known. The quota in 1999, 6,000, was lowered in 2000 to 3,500, which was still nearly 5% of the population if the Greenpeace count is correct. In 2013–2014, the hunting quota was set at 2,500. In addition, new techniques, such as netting breathing holes and seal dens to catch pups, have been introduced. In 2001, a prime seal pelt would bring 1,000 rubles at market. In 2004–2006, about 2,000 seals were killed per year according to official Russian statistics, but in the same period another 1,500–4,000 are thought to have died annually due to drowning in fishing gear, poaching, and the like. In 2012–2013, it was estimated that 2,300–2,800 were hunted per year (combined legal hunting and poaching). Some groups have pressured for higher hunting quotas.
Another problem at Lake Baikal is the introduction of pollutants into the ecosystem. Pesticides such as DDT and hexachlorocyclohexane, as well as industrial waste, mainly from the Baikalisk pulp and paper plant, are thought to have exacerbated several disease epidemics among Baikal seal populations. The chemicals are speculated to concentrate up the food chain and weaken the Baikal seal's immune system, making them susceptible to diseases such as canine distemper and the plague, which was the cause of a serious Baikal seal epidemic that resulted in the deaths of 5,000–6,500 animals in 1987–1988. Small numbers died as recently as 2000, but the reason for their deaths is unclear. Canine distemper is still present in the Baikal seal population, but has not caused mass deaths since the earlier outbreaks. In general, levels of DDT and non-ortho PCB have declined in the lake from the 1990s, levels of mono-ortho PCB are unchanged, and the level of perfluorochemicals have increased. Industrialization of the area near Lake Baikal is increasing and future monitoring is necessary. At present, Baikal seals show lower levels of contaminants than seals of Europe and North America, but higher than those in the Arctic.
The most serious future threat to the survival of the seal may be global warming, which has the potential to seriously affect a closed cold-water ecosystem such as that of Lake Baikal.
The only known natural predator of adult Baikal seals is the brown bear, but this is not believed to occur frequently. The seal pups are typically hidden in a den, but can fall prey to smaller land predators such as the red fox, the sable and the white-tailed eagle.