It will cost the city millions to repair all the damage done by two recent major floods, including parts of the waterfront trail it will likely have to completely rebuild.

Hundreds of metres of that are still underwater. - Dan McKinnon, general manager of public works

The city will have to spend as much as $5 million to undo the damage from flooding that resulted from heavy rain storms in late April and early May, said Dan McKinnon, general manager of public works.

That includes repairing and repaving parts of the Waterfront Trail, which sees nearly 13,000 users per week and is heading into its most popular season.

It also eroded breakwalls and washed away landscaping on the Trail, which runs from Bayfront Park into Cootes Paradise, ending at Princess Point.

In the east, water has also washed away parts of Confederation Park beach, McKinnon said.

"Hundreds of metres of that are still underwater," McKinnon said of the Waterfront Trail.

The city will also have to clear away "significant debris" that's washed up from the lake, he said.

None of this can happen until the water recedes, and that will take a while.

There's been record rainfall in Hamilton so far this year. On April 20, a full month of rain fell on Dundas in particular, when basements and businesses flooded. Hamilton usually gets 73 mm in April, Environment Canada says. In one day, 72.4 mm fell at the Royal Botanical Gardens.

Then in early May, another rain storm partially flooded streets near Hamilton's waterfront. The ground was already saturated from the previous rainfall, the city said. Hamilton saw 82 millimetres of rain in the first week of May, which is more than the monthly average of 80 millimetres Environment Canada said.

Now McKinnon is coming up with "a rough budget" of how much it will cost the city to fix the problems.

"My guess is it won't exceed $5 million, but it'll definitely be in the millions," he said.

The high water levels have brought other surprises, including fish in unexpected places.

The city has two combined sewer overflow (CSO) tanks at Eastwood and Bayfront parks, McKinnon said. Hamilton Harbour water levels are so high, the water is spilling into the overflow tanks.

Some of those fish have gotten into the sewer system and made their way to the Woodward wastewater treatment plant, McKinnon said.

"I've seen fish at the wastewater plant," he said. "There's probably fish swimming in the CSO tanks as we speak."

samantha.craggs@cbc.ca | @SamCraggsCBC