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Ward's Island resident Alison Gzowski walks along Ward's Island Beach where sand used to stretch out beyond the lifeguard stand. The Toronto Island has been hit hard by flooding as heavy rains have caused Lake Ontario water levels to rise. The city has closed access to much of the island, including Centre Island.Deborah Baic/The Globe and Mail

As part of an emergency measure to begin Wednesday, more water from Lake Ontario will flow into the St. Lawrence River than ever before, as officials put into effect a flood-reducing strategy expected to delay shipping schedules and keep captains and others affected by high water levels on anxious watch.

At a meeting Monday, the International Lake Ontario-St. Lawrence River Board agreed to increase the flow rate over the Moses-Saunders Power Dam near Cornwall, Ont. – from 10,200 to 10,400 cubic metres a second. That's the equivalent of four Olympic-sized swimming pools draining into the river every second.

Though Lake Ontario levels seem to be receding, the emergency measure will be in effect for at least a 72-hour trial period. Officials will determine whether the river, and the ships that navigate it, can handle the swelling current as they attempt to drain Lake Ontario – which has seen record depths in recent weeks. The change in flow rate over the dam means new measures for cargo ships: reduced speeds; one-way sailing; and the use of a tugboat around the Iroquois Lock, at Brockville, Ont., where the current is expected to be the most problematic.

Read more: Charting Canada's troubled waters: Where the danger lies for watersheds across the country

Wallace James, a ship captain with Algoma Central, said the higher water and stronger currents have made it a challenge to navigate the St. Lawrence Seaway. Mr. James, a captain for 16 years, called conditions "terrible." He said strong currents around locks near Montreal made it difficult to steer his 225-metre vessel into a channel on his way upriver to Lake Ontario this week.

"It almost turned us around," Mr. James said aboard the Algoma Strongfield, which was docked in Hamilton Tuesday to unload 29,000 tonnes of iron ore.

"This is an exceptional scenario," said Andrew Bogora, spokesman with the St. Lawrence Seaway Management Corporation. Mr. Bogora said his group will continue to talk with captains as they navigate the river under the high-flow conditions, to gauge any difficulties vessels may encounter while travelling between Montreal and Lake Ontario. Mr. Bogora said captains are under strict guidelines to monitor the wake their vessels produce, so as to minimize any possible or further damage caused to property and shorelines affected by water levels.

Jacob Bruxer, a senior water resources engineer with Environment Canada, said Lake Ontario levels have actually decreased by about six centimetres since the start of June. Mr. Bruxer, who has been providing technical expertise to the board, said the lake peaked at 75.88 metres above sea level on May 29.

Mr. Bruxer said the increase in flow rate over the Moses-Saunders dam will shave about 0.6 centimetres from Lake Ontario's depth each week. While that may not sound like much, he said every little bit counts. Mr. Bruxer said the increased flow, combined with Lake Erie's decreasing water level – he said it is "drying out" – and the warming the region will experience as summer approaches, will further help the high-water situation. He said it will likely be weeks before water levels return to normal.

Mr. Bruxer said the decision to increase the flow rate into the St. Lawrence River is in part because downstream Quebec, in areas that have seen widespread flooding, also appears to be drying out.

"We are well aware of and very concerned by the impacts both upstream and downstream," he said. "We are kind of doing all we can and just hoping for dry weather."

And while water levels in Lake Ontario have been responsible for flooded beaches, flooded downtown Toronto condos, and the closure of the Toronto Islands, rising shorelines on the U.S. side of the lake are also causing concern.

"Counties on the south shores of Lake Ontario have declared states of emergency," said Arun Heer, the U.S. secretary for the International Lake Ontario-St. Lawrence River Board. "Erosion, flooding, things of that nature to homes and business and marinas are all being affected."

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