The main threat to the Saimaa seal consists of disturbance (especially by recreational snowmobiles in winter that disturb the pups), pollution and habitat destruction by development on the shores of Lake Saimaa. Despite the preventive measures, there is occasional net entanglement of the seals. Pollution, especially with organochlorines still poses a threat to this population. With the increased boat traffic and tourism there is an increase of disturbance. The building of summer cottages around the lake can lead to habitat destruction. The water level control in the lake for the power plant can cause the breaking of the ice in the breeding season, with disastrous effects for the newborn pups. An overall increased pressure on the lake may reduce the room for the seals.
The Saimaa seal is found only in Lake Saimaa in South-East Finland. There are 2 main breeding areas in the lake (Linnansaari and Kolovesi). Since this species lives rather isolated, there is no real competition and there are no natural predators. This species has been protected since 1955. To prevent incidental kill of this rare seal, fisheries are banned from the breeding areas.
A 1983 estimate of the population put it at 100-150 animals, rising in 1988 to an estimated 150-160 seals and in 1991 between 160 and 180 seals. Of those seals, 38-40 were sexually mature females. The number of pups born each year ranges from 18-26. For 1995, the population was estimated at over 200 seals.