Two pumps at Horbury Bridge in Wakefield have been managerless for three years since the company previously responsible for maintaining it, Carrillion, collapsed.
The station was later found to have failed and contributed to the unprecedented flooding seen around the Reid Park beck in Horbury in early 2020.
The local authority says it hopes having the system functioning will reduce the risk of homes being washed out in future.
Speaking at a Cabinet meeting on Tuesday where the move was agreed, Horbury and South Ossett councillor Darren Byford said residents were still affected by last year's extreme weather.
He said: "This shows that the council is listening to people. People living in the Reid Park area told us there was an issue down there.
"This has had a devastating effect on people there. Some of the residents, who have become very good friends of mine over the last 12 months, are still living the trauma of those floods that happened during the storms."
The station was originally built in the early 1990s as part of a new housing development in the area.
The pumps were designed to deal with surface water on the estate and to divert water from the beck into the River Calder when the beck was at risk of overflowing.
Housing developer Hassall Homes was originally responsible for the system before passing it onto Carillion in 2016.
Councillor Matthew Morley said: "The pumping station never belonged to the council, but we had the storms at the back end of 2019, it did start to fail.
"Unfortunately, we all know that in January and February last year while we were looking to improve it, the storms came back again.
"I'm pleased to say the station is now fully operational. Residents can rest assured we will be supporting them and we'll do what needs to be done to take surface water away from the area."
Local Democracy Reporting Service