The idea was audacious. In 1968, responding to the International Joint Commission's 1965 call for studies on transboundary pollution in the lower Great Lakes, the Province of Ontario and the Government of Canada set aside 46 small, deep lakes and their catchment areas in the Precambrian Shield. Dr. W. E. Johnson of the Freshwater Institute in Winnipeg had convinced the government that the only way to obtain unimpeachable evidence about eutrophication was to deliberately pollute pristine lakes under controlled conditions. Dr. John Vallentyne, Scientific Leader of the Eutrophication Section from 1966 to 1972, assembled a world-class team, recruiting a young scientist named David Schindler. Schindler would direct ELA projects from 1968 to 1989 and become one of the world's leading limnologists. In 1969, the first fertilization experiment began on Lake 227. The whole-ecosystem approach -- treating each lake as a single, manipulable unit -- was revolutionary.

The Lake 226 experiment was elegant in its simplicity. Researchers divided the lake with a curtain and fed one basin carbon and nitrogen, the other carbon, nitrogen, and phosphorus. The phosphorus basin erupted in algae; the control side stayed clear. That aerial photograph convinced policymakers where years of lab studies had failed. Phosphate bans in detergents followed across North America. But the discoveries kept coming. ELA research produced important evidence on the effects of acid rain, revealed that phosphates from household detergents cause algal blooms, showed how mercury accumulates in fish, and demonstrated that flooding wetlands for hydroelectric dams increases greenhouse gas production. By the time Schindler received the Gerhard Herzberg Gold Medal for Science and Engineering in 2001, his ELA work had also demonstrated the cumulative impacts of global warming, acidification, and ozone depletion on boreal lakes. The station has generated 745 peer-reviewed scientific articles, 126 graduate theses, and earned its scientists the Stockholm Water Prize and the Tyler Prize for Environmental Achievement.

In 2012, the Canadian federal government defunded the Experimental Lakes Area through the omnibus Bill C-38. The decision stunned the scientific world. The journal Nature called it "disturbing" and noted it was "hard to believe that finance is the true reason" for the closure. Five major scientific organizations, including the Ecological Society of America and the International Society of Limnology, wrote an open letter of protest. NDP MP Philip Toone pointed out that the internationally recognized program would cost more to close than the $2 million the government hoped to save. In March 2013, the Department of Fisheries and Oceans began dismantling research cabins without notifying scientists whose personal belongings remained inside. A coalition of citizens and scientists, spearheaded by researcher Diane Orihel, mobilized to save the facility. Ontario Premier Kathleen Wynne pledged provincial support after the federal government walked away.

On April 1, 2014, the International Institute for Sustainable Development signed three agreements with the governments of Ontario and Canada to become the long-term operator of what is now called IISD Experimental Lakes Area. The transition was not without controversy -- former ELA Chief Scientist John Rudd argued that IISD lacked the scientific expertise to run the facility, and Elizabeth May, who had served on IISD's board for nine years, acknowledged the think tank was not necessarily the ideal operator. But keeping ELA open was paramount. Since taking over, IISD-ELA has expanded its research portfolio into urgent new territory. In 2014, researchers added nanosilver particles to Lake 222 and discovered bioaccumulation in yellow perch and northern pike, with perch metabolic rates declining for a full year. In 2017, a diluted bitumen study found that phytoplankton and zooplankton communities crashed by more than 70 percent after simulated oil spills. In 2021, researchers began dosing lake enclosures with the antidepressant venlafaxine to study what happens when pharmaceutical runoff enters boreal waterways. Each experiment asks a question no beaker or tank can answer.