Harbour seals live in coastal areas many of which are heavily fished. As a result there are entanglement and by-catch issues which may be significant in some populations e.g. in northern Japan (Burns 2002). Over fishing, oceanographic regime shifts and global climate change may impact food chains harbour seals depend upon for prey.

Historically, there have been organized population reduction programs and bounty schemes in several range states of countries, largely because of perceived. Hunting and/or licensed killing to protect fisheries still occurs in Norway, UK and Iceland and subsistence hunting is allowed in Greenland and the United States (Alaska). In Greenland and Iceland there are indications that hunting is responsible for continuing population declines.

Mass die-offs from viral outbreaks have claimed thousands of harbour seals on both sides of the Atlantic, but most notably in Europe. In 1988 more than 20,000 harbour seals are estimated to have died from a phocine distemper virus (morbillivirus) epidemic in European waters (Dietz et al. 1989, Reijnders 1989). A similar outbreak in 2002 killed approximately 30,000 (Harkonen et al. 2006). Other disease outbreaks occurred both before and after this large epidemic in both Europe and the western North Atlantic, but resulted in much smaller levels of mortality. Influenza from an avian source killed approximately 500 harbour seals in the North-eastern United States in 1979 and 1980 (Burns 2002). Potential for exposure to disease is probably increased by the natural behaviour of this species to haul out on near shore and at coastal mainland sites. As a result terrestrial carnivores, waste from human populations as well as contact with human pets and feral animals associated with human populations creates an increased risk of exposure to communicable diseases.

Because many harbour seals live and feed in close proximity to large populations of humans they are exposed to and can accumulate high levels of industrial and agricultural pollutants in some parts of their range (see Reijnders 1978, 1985, 1986, Aguilar et al. 2002, Wang et al. 2007); while some northern populations have very low contaminant levels (e.g. Wolkers et al. 2004). Immuno-suppression is one affect regularly attributed to exposure to high levels of certain organochlorines and these and other contaminants probably contribute to poor condition and overall fitness of a number of animals in some areas. Both chronic oil spills and discharges and episodic large scale spills cause direct mortality and have long term impacts on harbour seal health and their environment. Some additional examples of threats and impacts to harbour seal populations are given below.

P. v. stejnegeri, of the western Pacific, numbers approximately 7,000 animals. Fishery related mortality in the small Japanese population is a cause for concern (Wada et al. 1991). However, low levels of human activity in the Kurils and protected status within nature reserves in the Commander Islands means that there is no obvious anthropogenic threat to the bulk of the population.

P. v. mellonae numbers only some 120-600 animals which are restricted to the Seal Lakes (Lac des Loups Marin) of the Ungava Peninsula, Canada. This subspecies is at risk due to low population numbers and unknown effects of James Bay II hydroelectric development which may reduce the water level in the seal lakes by 20 cm. This might have impacts on mortality of seals in winter and altered hydrographic conditions could potentially affect the seals’ prey.

P. v. richardii has shown dramatic reductions in the recent past in one large part of its range, Gulf of Alaska and Prince William Sound. Although part of this decline may be related to the effects of the Exxon Valdez disaster, the overall decline in Gulf of Alaska is unexplained.

Subpopulations of P. v. vitulina in the Northern UK have recently declined by around 50% in less than 10years. The cause of this decline is unknown. The Icelandic population has declined by 5% p.a. since 1980, which is thought to be due to direct hunting. Populations in Svalbard and the Baltic Sea, which are both small are protected. Competition with increasing gray seal populations may have been responsible for declines in the mid-latitudes and further increases in grey seal populations seem likely in the North Sea. Rapidly increasing development of offshore wind generated power means that the levels of industrial activity and noise are increasing in the foraging areas of resident harbour seals. To date, there is little information available to assess the potential impacts of such disturbance.

Historical population reductions of P. v. concolor along the USA coast were probably due to hunting that has now ceased. The rapid decline in the Sable Island population may have been due to a combination of shark predation (Lucas and Stobo 2000) and competition with grey seals (Bowen et al. 2003); the continued increase of grey seal populations in Canadian and US waters could produce a more widely spread decline.