This summer, as rain relentlessly poured down on the Great Lakes region, Detroit declared a rare state of emergency. The swollen Detroit River had spilled into the low-lying Jefferson Chalmers neighborhood – an event not seen near this scale since 1986.

Volunteers sandbagged the area as the city’s overwhelmed sewer system spilled raw sewage into the river, which connects Lake Huron and Lake Erie. Across the channel from Jefferson Chalmers, water damaged the historic boathouse on Belle Isle, a 982-acre island park that remains partly shut down because of flooding.

Meanwhile, in Duluth, Minnesota, the city is rebuilding after a powerful storm over Lake Superior damaged a popular pedestrian path, eroded acres of lakefront property and ravaged infrastructure along the shore.

About 800 miles to the east, floods hit Buffalo, New York, on Lake Erie in two of the last three years, while Lake Michigan’s historically high waters inundated parts of Chicago throughout the spring and summer months.

The havoc wreaked on communities bordering the Great Lakes is a result of their water level steadily rising over the last five years and spiking to record levels this spring and summer. In 2019, the lakes’ depths ranged from 14in to nearly 3ft above long-term averages, according to data from the US army corps of engineers. In June, water in the Lakes St Clair, Ontario, Superior and Erie set records for monthly mean levels, while Lake Michigan-Huron rose to 1in from its recorded peak.

That is leading to widespread damage in coastal cities, eroded shorelines and beaches and many other issues. The record levels come just five years after the lakes experienced historically low levels in 2014, and climate scientists say it is clear what’s fueling the drastic swing: the Earth’s rising temperatures.

“Bigger picture, it’s climate change,” said Richard B Rood, a professor in the University of Michigan’s department of climate and space sciences and engineering. “There’s no doubt that we are in a region where climate change is having an impact.”

Rood said the Great Lakes basin, which holds 90% of the nation’s freshwater, can expect similar shifts in the coming decades as world temperatures increase.

Climate scientists say a confluence of climate crisis-related issues resulted in this year’s levels. Warmer air over the Gulf of Mexico caused more evaporation, and that moisture pushed into the region during the spring and summer. Higher temperatures give the atmosphere more capacity to hold evaporated water, Rood said, which is why storms are dumping more rain than 50 years ago.

“When you’re in wet periods, you start to get persistent, basin-wide extreme precipitation,” he said.

The numbers back that up. By May, Cleveland, Ohio on Lake Erie’s shore saw more rainy days than any year since 1953. Muskegon, on Lake Michigan’s shore, experienced 7.45in more rainfall than average throughout the first eight months, while Sault Ste Marie on Lake Superior tallied about 9in more than average for the same period. Buffalo saw 34% more rain than typical.

The moisture rained down on ground and lakes already more saturated than usual because a January polar vortex brought frigid temperatures that prevented wintertime evaporation crucial to keeping water levels in check. Meanwhile, a heavy snow pack melted. pushing up levels even further.

“We’re seeing all these things that have an effect on the water cycle converge, which is why we’re having these enormous water volumes,” Rood said.

Though the region finally dried out a bit in August and water levels are slightly receding, the Great Lakes’ fall storm season is fast approaching. Fall is a time of high winds and the agency’s six-month forecast predicts levels will remain very high, thus there’s a strong likelihood for even more damage this year.

Coastal communities need to give the storms and fluctuating lake levels stronger consideration when building near the shoreline, said Richard Norton, an urban and regional planning professor at the University of Michigan. There’s still an inclination to build as close to the water as possible, which was especially a problem as levels began dropping in the early 2000s.

“People want to build in the most beautiful, fragile and dangerous places, and that’s challenging because of the way the lakes go up and down over time in a weird way … and it’s not a good idea,” Norton said.

The changes have an impact on the lakes’ ecosystems and natural environment, but it’s a mixed bag. While erosion is an issue, the basin is resilient and has withstood similar variability in the past, said Mark Breederland, an extension director with the environmental agency Michigan Sea Grant.

He said extreme fluctuations can benefit the coastal wetlands and some species, while other species, such as the endangered piping plover, face new threats. Meanwhile, the impact of continued climate change on the Great Lakes’ ecosystem is still unknown, Breederland said.

However, there is more certainty with water levels. Long-term, as temperature increases continue, the region will see levels “bouncing from low extreme to high extremes”, Rood said, though the lakes will eventually start to disappear if temperatures aren’t brought under control.

“If we don’t mitigate our emissions … and the temperature gets to a certain level, then it does become evaporation dominant,” he said.

• This article was corrected on 3 September 2019 to situate Buffalo, New York, on Lake Erie rather than Lake Ontario.