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A cargo ship makes it way through Lac St-Pierre on the St-Lawrence water way in Trois-Rivieres, Que., Tuesday, August 14, 2012.Paul Chiasson/The Canadian Press

The cross-border commission that regulates use of the Great Lakes says water levels on Lake Ontario and the St. Lawrence River should be allowed to rise and fall more naturally with the seasons – a fluctuation that would benefit damaged ecosystems but create problems for some U.S. property owners.

The International Joint Commission (IJC) released a final version of its Plan 2014 on Tuesday.

One U.S. politician has said the strategy, first unveiled last year, puts the interests of "muskrats and cattails" above those of homeowners. But the five members of the commission unanimously agree the harm to wetlands from the existing system of water-level controls must be curtailed.

The governments of the two countries will have to decide whether to adopt the commission's recommendations.

Since 1952, the commission has tried, with limited success, to restrict water fluctuations on Lake Ontario to a range of about 1.2 metres by increasing or cutting off the flow at a damn near Cornwall, Ont. The aim was to make lake levels more predictable for communities and property owners as well as for shipping and recreational boaters.

But that regulation did not take into account what would happen to the adjacent environment when the water was no longer permitted to rise naturally with the spring run-off and then drop through summer and fall. The result was significant damage to the natural habitat of northern pike, muskrat, turtles, frogs and other animals that live in and near the coastal plains.

"The current plan has caused substantial harm to the natural environment," Lana Pollack, the U.S. co-chair of the IJC, told reporters. "When the current plan was developed, the environment, conservation, habitat, was not a consideration. Now that it is, this is an attempt to reverse some, but not all of the harm by restoring some, but not all, of the natural variability of the lakes."

Under Plan 2014, which comes after 14 years of study and public consultation, the extreme highs and lows on the lake would continue to be controlled to the extent that that is possible; nature is still expected to deliver droughts and floods several times a century. But the lake would be allowed to drop by an additional 20 centimetres in the fall and winter, and to rise a tennis-ball's height higher in spring.

That is not expected to create major problems for people on the Canadian side, where the Ontario government has prohibited construction on flood planes since the devastation of Hurricane Hazel in 1954. In this country, an increased water-level range on Lake Ontario could actually extend the boating season and increase hydro generation by a small amount. It is not expected to have a significant impact on the levels of the other Great Lakes.

But on the U.S. side, particularly around Rochester, N.Y., some communities have been built on sand bars. Property owners in those areas would have to reinforce their breakwalls, and have told their politicians they fear their homes would be devalued and their harbour access reduced in the summer.

"It is fair to say we have had some criticism from people on the south shore who are in difficult locations," Gordon Walker, the IJC's Canadian co-chair, told The Globe and Mail. On the other hand, Mr. Walker said, the reaction in Canada to Plan 2014 "has bordered on enthusiastic support."

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