Biogenic reefs are three-dimensional carbonate structures which support biodiversity by increasing habitat heterogeneity in coastal ecosystems. Recently, polychaete reefs have been considered as ‘marine animal forests’ worthy of protection. The cosmopolitan species Ficopomatus enigmaticus is one of the most prominent providers of polychaete reefs in shallow and brackish waters, building circular bioherms that can reach 7 m in diameter. The effects of polychaete reefs on the environment can be positive or negative subject to their structural complexity and vary with local environmental conditions, and over time. The Coorong is a large temperate estuarine and lagoonal system with extensive polychaete reefs built by F. enigmaticus. The ecosystem functions of F. enigmaticus reefs were investigated including their value as habitat for macroinvertebrates and fish, their filtration effect on water quality, and how these functions vary with the structural complexity and age of the reef. Living polychaete reefs support bryozoans, polychaetes, crustaceans (decapods, amphipods, ostracods), gastropods and micro-bivalves. Small-bodied and juvenile fish use the sheltered polychaete reef habitats, and associations are species specific and vary seasonally. This study provides a novel insight into ecosystem functions of biogenic reefs and whether polychaete reefs may support the restoration of the Coorong, a Ramsar listed wetland.