The White Cart scheme was officially opened in October 2011 and has cut the risk of flood damage to around 1750 properties.
It has now been named the top civil engineering project at the British Construction Industry Awards in London.
Rivals for the award included work at Heathrow Airport and Paddington Station, new bridges in Derry and Battersea, and Bradford's City Park which has the UK's largest water feature.
The BCI awards are the UK's top accolades for overall excellence in building and civil engineering projects.
The £49million White Cart scheme included creation of new woodland, scrub, wet grasslands, ponds and other habitats.
Liz Cameron, the city council's executive member for jobs and the economy, said: "The project team involved in the design and construction of the scheme have created an exceptional and bespoke design."
Since 1908 there have been more than 20 significant floods in the South Side caused by relatively minor storms.
Within weeks of the scheme going into operation last year it had stopped two floods.