John received his B.Sc. in Marine Biology from McGill University in Montreal, Canada in 1977, and a M.Sc. in limnology from Brock University (St. Catharines, Ontario) in 1979. His Ph.D. in 1982 is from Queen's University in Kingston, Ontario. Following post-doctoral work in the High Arctic with the Geological Survey of Canada, he became a faculty member at Queen's University in 1984. John was promoted to Full Professor in 1991. He holds and has held adjunct appointments in Canada, the United States and China.

John founded and now co-directs the Paleoecological Environmental Assessment and Research Laboratory (PEARL) at Queen's University, a group of about 30 paleolimnologists (researchers studying long-term changes in aquatic ecosystems using lake and river sediments as archives of long-term natural and human-related environmental change) working throughout the world on a variety of limnological and paleoecological problems. Recent projects include studying the long-term effects of lake eutrophication, acidification, contaminant transport, calcium decline, fisheries management, and a large body of work on climate change with a special focus on the Arctic. 

John has over 700 journal publications and book chapters to his credit. He has edited and authored 24 books, including one textbook on paleolimnology, now in its second edition, and co-authored a textbook on ecology, also in its second edition. He has one other book in preparation. Smol has over 55,000 Google Scholar citations. Smol has lectured on all seven continents, and has authored over  1200 conference presentations, which include ~150 keynotes and plenary lectures. For example, he was the 2008 Rutherford Lecturer at the Royal Society (London) and presented the inaugural Thienemann Lecture at the Leibniz Institute of Freshwater Ecology (Berlin, Germany) in 2016. Smol is a frequent commentator on environmental issues for radio, television, and the print media.

PEARL's paleolimnological work was used extensively in the acid rain debates, and John received a citation from the US government for "outstanding contributions" to the NAPAP program. John was awarded an N.S.E.R.C. E.W.R. Steacie Memorial Fellowship in 1990. In 1992 he was awarded the Botanical Society of America Darbaker Prize, and in 1993 John, along with his lab, was presented with the North American Lake Management Society (NALMS) Research Award. In 1993 he was also awarded the National Research Council's Steacie Prize, as Canada's most outstanding young scientist or engineer. In 1994, he received an award from the Atomic Energy of Canada, Ltd., and was presented with the Queen's University Prize for Excellence in Research. In 1995 he was awarded the Rigler Prize from the Society of Canadian Limnologists and the Canada Council Killam Fellowship (1995-1997). In 1996, he was elected as a fellow of the Royal Society of Canada, Academy of Science, and in 1997 he received the University of Helsinki Award Medal, as well as the Geological Association of Canada's (GAC) Past-President's Medal (later renamed the G.W. Hutchinson Medal) for outstanding contributions to the geosciences. The GAC also elected him as one of their Distinguished Fellows. In 1998 and 2001, he was chosen to receive the Best Professor Award for excellence in undergraduate teaching by the Queen's Biology DSC, and in 2000 he received the W.T Barnes Teaching Excellence Award. In 1999 he was awarded the Turku Academia Medal, the Canada Research Chair in Environmental Change in 2000, and in 2001 he was presented with the Miroslaw Romanowski Medal from the Royal Society of Canada for contributions to the resolution of scientific aspects of environmental problems. In 2002, he was granted an Ontario Distinguished Researcher Award (ODRA). St Francis Xavier University conferred John with the honorary degree of Doctor of Laws (LLD) in June 2003, in recognition of his work on aquatic ecology and environmental change. In November 2003, John was presented with the NSERC Award for Excellence. In December 2004, John was awarded the NSERC Gerhard Herzberg Gold Medal, as Canada's top scientist or engineer. In June of 2005, John was awarded the Canadian Quaternary Association's most meritorious award, the WA Johnston Medal for professional excellence in Quaternary science. John was presented with two additional teaching awards offered by Queen's University in 2006: the inaugural Award for Excellence in Graduate Supervision, and The Chancellor A. Charles Baillie Teaching Award. In addition, he was listed by Thompson Scientific as an ISI Highly Cited Researcher. In 2007, John was presented with the G. Evelyn Hutchinson Award from the American Society of Limnology and Oceanography "For outstanding contributions and leadership in bridging paleolimnology with limnology, ecology, and the environmental sciences, as well as his seminal work on polar limnology and environmental change." The University of Helsinki conferred John with an honorary PhD in May 2007. Later that year, he was awarded the T. Geoffrey Flynn Advancement Champion Award, Queen's University's highest award for service, for his scientific outreach and education work with the public. In 2008, John was selected by the Royal Society (London) to be "The UK-Canada Rutherford Lecturer", and later that year he, along with his brother J. Blais, were chosen as Canada's Environmental Scientists of the Year by the Royal Canadian Geographical Society. In November, John was presented with his second medal from the Royal Society of Canada -- the Flavelle Medal for outstanding contributions to biology. In 2009, the Society for Teaching and Learning in Higher Education (STLHE) presented John with a 3M National Teaching Fellowship, considered by many to be Canada's highest teaching award. Shortly afterwards, John won the 2009 Killam Prize in the field of natural sciences, which is the highest career achievement award presented by the Canada Council, and later that week the Premier of Ontario presented him with the Premier's Discovery Award  for the Life Sciences and Medicine, the province's highest award for academic achievement. He was also presented with the Canada Foundation for Innovation Leaders Opportunity Fund Award. In 2010, John was made a Fellow of the Royal Canadian Geographical Society, and then following a nation-wide competition, John was chosen by Nature as Canada’s Top Mid-Career Science Mentor. In 2012, the Chinese Academy of Sciences named Smol one of their twenty Einstein Professors. He was also named as one of Brock University’s top 35 alumni, and was presented with the Brock University Alumni of Distinction Award. Also that year, the Association for the Sciences of Limnology and Oceanography (ASLO) awarded John a second honour – the Ramon Margalef Excellence in Education Award for “his outstanding work with educational duties of teaching undergraduate courses and mentoring graduate students”, and he was co-winner of the Cowles Award from the Association of American Geographers, for the best journal paper or book published in 2011 on biogeography. Also in 2012, the University of Waterloo presented Smol with an honorary Doctor of Science (DSc), and he was also presented with a Queen Elizabeth II Diamond Jubilee Medal  in recognition of his contributions to Canada. In 2013, John was awarded the inaugural Science Ambassador Award from the Partners in Research National Awards, was named an Honorary Professor at Yunnan Normal University (Kunming, China), was awarded the Weston Family Prize for Lifetime Achievement in Northern Research, the largest prize of its kind, and was named by Canadian Geographic Magazine as one of nine Change Makers - defined as Canadians changing the world in 2013. In addition, the Governor General  named John an Officer of the Order of Canada – the country’s highest civilian honour. In 2014, he along with Jules Blais were jointly awarded the NSERC Brockhouse Canada Prize for Interdisciplinary Research in Science and Engineering, Canada’s highest honour for interdisciplinary research excellence. In 2015, John was chosen by the Council of Ontario Universities as one of the top 50 researchers who had conducted game-changing historical moments in Ontario research over the past 100 years; the Erebus Medal from the Royal Canadian Geographical Society; the International Ecology Institute (ECI) Prize in Freshwater (Limnetic) Ecology, for “…  leadership in bringing paleolimnology to bear so effectively on the urgent environmental problems we face today”; named by the Royal Canadian Geographical Society as one of Canada’s Greatest Explorers -100 of the nation’s top modern-day trailblazers; named a Research Professor at Lanzhou University (China); the Martin Bergmann Medal for Excellence in Arctic Leadership and Science from the Royal Canadian Geographical Society; and the McNeil Medal for the Public Awareness of Science from the Royal Society of Canada. In 2016,  he was named the 2016-2017 UCLA Canadian Scholar in Residence, an Honorary Research  Professor and then a Distinguished Professor, at South China Normal University (Guangzhou, China), presented the inaugural Thienemann Lecture at the Leibniz Institute of Freshwater Ecology (Berlin, Germany), was named  one of the inaugural Sustaining Fellows of the Association for the Sciences of Limnology and Oceanography (ASLO), and the Northern Science Award  and the Centenary Medal from Polar Knowledge Canada (Canadian federal government), as well as being presented two additional honorary doctorates: a Doctor of Laws (LLD, honorary) from Mount Allison University and the inaugural Doctor of Science (DSc, honorary) from Ryerson University. In 2017, he received his 6th honorary degree – a DSc from Western University, was co-winner of the NALMS Jim LaBounty Award.  In 2018, he was presented with the Canadian Association of University Teachers (CAUT) Distinguished Academic Award, recognizing excellence in the three domains of academic life: teaching, research, and service. In addition, he was inducted as a Fellow of the Royal Society (FRS) and received the 2018 Naumann-Thienemann Medal of the International Society of Limnology (Societas Internationalis Limnologiae, SIL) -  “the highest honor that can be bestowed internationally for outstanding scientific contributions to limnology”, as well as the Sandford Fleming Medal from the Royal Canadian Institute for Science (RCIS). “For outstanding achievements in promoting knowledge and understanding of science …”. In 2019, the Governor General of Canada presented Smol the Polar Medal for “extraordinary services in the polar regions and Canada’s North …”, and in 2020 Queen’s University designated him a Distinguished University Professor , the highest research-related honour the university can bestow on an individual and a title preserved for ~1% of the university’s faculty.  Also in 2020, the Royal Canadian Geographical Society awarded Smol their senior medal – the Massey Medal – to “recognize outstanding career achievement in the exploration, development or description of the geography of Canada”. In 2021, Smol was named an Expertscape World Expert on Lakes (one of the top 0.1% of authors publishing on lakes over the last 10 years) and added to the Reuter’s Hot List (one of the top 1,000 most influential climate scientists). In 2022, in Argentina, he was awarded the International Paleolimnology Association (IPA) Rick Battarbee Lifetime Achievement Medal, the major award of the IPA. In April 2023, King Carl XVI Gustaf of Sweden presented Smol with the 2023 Vega Medal, given out about every three years since 1881 by the Swedish Society for Anthropology and Geography (SSAG) for outstanding scientific contributions to Physical Geography. Also in 2023,he was awarded his 4th medal from the Royal Society of Canada – the Sir John William Dawson Medal -- for important and sustained contributions in two domains (in his case, geology and biology) of interdisciplinary research, and thus making him the first scientist to win more than 2 individual medals from the RSC since its foundation in 1882. In November 2023, John was appointed to the Order of Ontario – the province’s highest civilian honour. Research.com identified Smol as Canada's top earth scientist. In 2024, he was awarded his 7th honorary doctorate, a D.Sc. from Acadia University; the "A.C. Redfield Lifetime Achievement Award from the Association for the Sciences of Limnology and Oceanography (his 4th recognition from ASLO) in Madison, Wisconsin; the Award of Excellence from the Phycological Society of America in Seattle, Washington; and the American Quaternary Association (AMQUA) Distinguished Career Award in Salt Lake City, Utah.