The Toronto native joined a Sierra Club protest against nuclear testing in 1969. He was an early and influential member of Greenpeace, crewed and skippered for it, and later was a board member. Watson argued for a strategy of direct action that conflicted with the Greenpeace interpretation of nonviolence, was ousted from the board in 1977, and subsequently left the organization. That same year, he formed Sea Shepherd Conservation Society. The group is the subject of a reality show, Whale Wars.
He also promotes veganism, voluntary human population control, and a biocentric, rather than anthropocentric, worldview.
Watson's activities have led to legal action from authorities in countries including the United States, Canada, Norway, Costa Rica, and Japan. After skipping bail following an arrest in Germany, on August 9, 2012 Interpol issued a red notice requesting his arrest. A second red notice was issued on September 14, 2012, this time at request from Japan.