Coastal Partners, which is carrying out the £58m North Portsea Island Scheme upgrades, won in the coastal management category at Wednesday's Flood & Coast 2022 Conference and Excellence Awards.
The organisation's head of service Lyall Cairns said he was 'immensely proud' of the recognition.
'These flood defences have the potential to become a blueprint for future environmentally-driven sea defences,' he said. 'As a groundbreaking "greening the grey" solution, they benefit the local ecology, adapt to climate change and protect the community.'
The scheme, which stretches from Milton Common to Tipner, started in 2015 and is due to be completed in 2025 and includes the first 'large-scale' use of an ecoformliner in the UK.
Ecoformliners are a reuseable mould for the finish of seawalls and are aimed at improving coastal habitats while also strengthening their structure by encouraging the growth of vegetation.
A special, UK-first design was created for the defences around Langstone Harbour with the support of the Environment Agency and this was recognised on Wednesday for its 'vast environmental benefits'.
Work on this section of the seawall began in April last year and is due to be completed in the autumn of next year, however Coastal Partners said the early stages of the new habitat had already began to establish itself.
It added that both Thames Estuary and Mumbles flood defence schemes were now considering similar approaches.