The study, conducted by the Mowat Centre for the Council of the Great Lakes Region, said water levels in the Great Lakes — which hold about 20 per cent of the world's surface freshwater supply — and St. Lawrence River "fell dramatically" in 1997-98.
Since then, the basin has experienced the longest extended period of lower water levels since the U.S. and Canada began tracking levels in 1918.
Mark Fisher, who heads the council, said there's a "very real future" where the region could be plagued by low water trends.
"When you look at the last 13 years, we've gone through the longest period of low water levels in our history," he said.
Lake Michigan-Huron had the lowest water level ever recorded for the lake in January 2013.
Water levels in the St. Lawrence River have also diminished, recorded at below historic averages for 78 per cent of the total months from 1998 to 2012.
Climate change is a closely related issue and requires input on local, provincial and federal levels, Fisher said, adding that collaboration between Canada and the U.S. will be essential to safeguard the future of the Great Lakes and St. Lawrence basin.
"The challenge that people have is (climate change) is gradual, it's incremental, it's hard to see," he said. "So when water levels go back up, they say the problem has gone away."
The report, titled Low Water Blues, found that while water levels have "rebounded" since 2013, due to factors including cooler temperatures in winter, it's "unclear" if this is the beginning of a trend.
"The general rule is that there is more evaporation and less precipitation, so less water in the system," Fisher said, explaining that only one per cent of the waters of the Great Lakes are renewed on an annual basis by precipitation.
The economic output of the Great Lakes Region is C$5.25 trillion, or around 28 per cent of the combined Canadian and U.S. economic activity.
The report said lower water levels in the Great Lakes would impact industries including hydroelectricity and commercial shipping, as well as recreational boating and fishing and property values near the shores.
Rod Jones, president and CEO of the Canada Steamship Lines group, said the shipping industry needs to plan for a "sustainable future."
The study found that low water levels could have an economic impact of just over C$2 billion from now until 2050 on commercial shipping and harbours. For recreational boating and fishing, the cost could reach more than C$13.74 billion.
Jones explained that "choke points," such as the Welland Canal which connects Lake Ontario and Lake Erie, determine whether or not ships can enter the Great Lakes and St. Lawrence seaway.
High water levels are more cost effective for shipping because ships are able to carry heavier cargo, he said.
The Great Lakes ability to compete on the global shipping market is already diminished because of large terminals elsewhere, Jones said.
In the past, he said, the industry focused on dredging to improve efficiency, but now there is more awareness about the impact of climate change.
"We can't afford to have the seaway shallow," he said, adding that now the onus is on industries to evaluate their own environmental footprint.
"When we do put an economic and environmental argument together, it's much more compelling to the public," he said, adding that because the basin represents a "small, precious resource," Canadian industries are forced to act.
"We're in a much smaller area, and we've got more scrutiny from the public and the government."
Fisher said the study's projections are "conservative," given that researchers did not look at indirect effects or how low water levels could impact human health, commercial fishing or the manufacturing sector.
"The costs would only get much larger if we calculated in the indirect costs," he said.
The next step is a cost-benefit analysis of adaptation measures and mitigation strategies in responding to climate-change induced low water levels, Fisher said.
"Climate change is real, it's happening today, the potential economic impact of climate change particularly on water levels is significant," he said. "We need to pay attention because at the end of the day, while the Great Lakes are vast, they are a finite resource."