Quebec's Prime Minister Philippe Couillard said that the levels had begun easing off on Tuesday.
Trudeau asked Canadians to be generous in helping their compatriots in need.
Halifax-based frigate HMCS Montréal, which was to be in Montreal Friday as part of the city's 375th anniversary ceremonies, was reassigned and will be in Trois-Rivières from Thursday morning until Saturday to help with flood relief efforts.
"We know the ceiling probably has to be adjusted", he said.
The military is deploying another 600 soldiers to help deal with the flooding in Quebec, amid fears of more heavy rains this weekend.
"As the minister of defence has said, with the military, we arrive quickly but we leave slowly", he added.
He said $800,000 has already been distributed, with more to come from the province and the Red Cross.
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The Canadian Red Cross has set up a relief fund, with the federal government contributing $1 million and the Quebec government $500,000.
One of the areas hardest-hit by spring flooding is the Gatineau region in Quebec and that's where the prime minister and that province's premier got a first-hand look at the damage today.
"We are now entering a period of falling water levels", he said, but warned that this did not mean flooded areas would be easily accessible again even in the coming days.
Meanwhile, Public Security Minister Martin Coiteux told the same news conference that 3,882 residences in the province have now been affected by the recent floods.
The floods have claimed at least one life in the province - a man whose auto ended up in a surging river in the eastern Gaspe region. Authorities continued their search Thursday for a two-year-old girl who disappeared in the same incident.
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Several rivers and lakes had reached near 50-year peak levels in Quebec province, between Gatineau in the Canadian capital region and Montreal, 200 kilometres (125 miles) downstream.
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