Watson was the Director of the Science Division and Chief Scientist for the Office of Mission to Planet Earth at the National Aeronautics and Space Administration (NASA). Watson then became Associate Director for Environment in the Office of the President of the United States in the White House.
In 1996, Watson joined the World Bank as the Senior Scientific adviser in the Environment Department, became Director of the Environment Department and Head of the Environment Sector Board in 1997 and is currently the Chief Scientist and Senior Adviser for Sustainable Development. He took up a position as Chair of Environmental Science and Science Director of the Tyndall Centre at the University of East Anglia, United Kingdom, in August 2007 and joined the British Government's Department for Environment, Food and Rural Affairs (Defra) as Chief Scientific Adviser in September 2007.
Watson had a role in the regulation efforts related to both ozone depletion and global warming. The Montreal and Vienna conventions were installed long before a scientific consensus was established. Until the 1980s EU, NASA, NAS, UNEP, WMO and the British government had dissenting scientific reports. Watson played a role in the process of unified assessments and did so as well for the IPCC.
He was Chairman of the Global Environment Facility's Scientific and Technical Advisory Panel from 1991 to 1994, Chair of the Intergovernmental Panel on Climate Change (IPCC) from 1997 to 2002 and Board co-chair for the Millennium Ecosystem Assessment from 2000 to 2005. He was then Director of the International Assessment of Agricultural Science and Technology for Development which ran from 2005 to 2007, and had previously been co-chair of the International Scientific Assessment of Stratospheric Ozone for their reports from 1994 to 2006. He has been Chair or co-chair of other international scientific assessments, including the IPCC Working Group II, the United Nations Environment Programme/World Meteorological Organization (UNEP/WMO), and the UNEP Global Biodiversity Assessment.
Watson was knighted in the 2012 New Year Honours for his government service.
He is currently Director of Strategic Development for the Tyndall Centre for Climate Change Research at the University of East Anglia.
On 29 February 2016, Watson was elected Chair of IPBES at the Fourth Plenary of that organisation after having served as its vice-president before.