Hobsons Bay supports significant ecosystems including marine areas, wetlands, woodlands and grasslands. It is also boasts the internationally recognised, Ramsar listed Cheetham Wetlands. A total of five water-ways run through the municipality including Skeleton Creek, Laverton Creek, Cherry Creek, Kororoit Creek and Stony Creek. 

These open spaces provide a home to a diverse range of ecosystems that provide habitat to an impressive range of flora and fauna, including many rare and threatened species. These unique assets are managed by Hobsons Bay City Council, Parks Victoria, Melbourne Water and the Department of Environment Land Water and Planning.