The history of whaling in British Columbia has had lasting effects on cetacean populations. From 1866 to 1875, European whaling ships targeted grey whales and North Pacific right whales for their oil, depleting their numbers to the point of commercial inviability. Humpback whales were also hunted during this time, but their population has since recovered. The introduction of steam-powered ships and explosive harpoons in the 20th century led to the first and second modern era of whaling, resulting in the removal of at least 24,862 whales from B.C. waters by 1967.

The North Pacific right whale population remains critically endangered despite legal protection, with an estimated 30 individuals remaining. Blue whales and fin whales were heavily targeted, with their populations severely reduced. Sei whales, once common in B.C. waters, are now scarce, and only around 100 individuals are taken annually by Japan. Grey whales have shown a slow recovery, with around 20,000 individuals estimated in the Eastern North Pacific. Humpback whales have made a remarkable recovery, with their population rebounding to at least 18,302 whales in the North Pacific.

Sperm whales were heavily hunted for their oil, but their population in the North Pacific now stands at approximately 80,000 and is not considered at risk. Killer whales were not targeted by commercial whaling but were impacted by live-capture operations. Northern and southern resident killer whales are listed as threatened and endangered, respectively, in B.C.

Today, aboriginal subsistence whaling continues in certain regions, recognized by the International Whaling Commission as different from commercial whaling. Special Permit Whaling, also known as "scientific whaling," is still practiced, with Japan issuing permits for research purposes. Japan's new proposal for a special whaling program in the North Pacific has faced criticism from the IWC's expert panel.