But the work has meant regeneration of the area with three housing developments worth £15m under way creating more than 230 new homes, the agency said.
A further six sites for more than 350 homes and a regional AI hub are going through the planning process with the council, it added.
The work involved repairs and upgrades to over 500m (1,640ft) of the channel, extending its lifespan for another 60 years.
Brown trout and chub found during construction can now move freely along the waterway after the reopening of 6.5km of the brook for fish migration, it said.
Mark Swain, West Midlands flood risk team leader at the Environment Agency, explained that the work was essential to mitigate flood risks.
“We are already seeing the effects of climate change in the UK,” he said.
“We’re working to reduce flood risk for communities, with climate change projection built into the design of any scheme to ensure they are fit for the future.”
Councillor Finlay Gordon-McCusker, cabinet member for regeneration, transport and infrastructure at Stoke-on-Trent City Council, said the completion of the project was a milestone and meant long-term protection for homes and enabled regeneration of brownfield sites.
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