Shellfish reefs have experienced enormous declines from temperate and tropical coastal systems worldwide. This global loss and their socio-ecological value has motivated extensive shellfish reef restoration efforts in recent years. However, successful restoration requires baseline data on ecosystem characteristics, drivers of decline, and past management outcomes. Historical reviews can be essential for developing evidence-based restoration strategies and fostering stakeholder support, particularly for lost and understudied shellfish reefs. We used over 3,000 archival records to reconstruct the historical distribution, ecological interactions, and management of South Australia’s lost flat oyster (Ostrea angasi) and razor clam (Pinna bicolor) shellfish reefs. Our analyses demonstrated that mixed-species shellfish reefs historically characterised South Australia’s seascape, but harvesting removed >76,000 bags of oysters by the 20th century. Shellfish reefs also initiated the state’s earliest marine management and restoration attempts from 1853 onwards, with mixed success. The statewide loss of Ostrea angasi reefs within two centuries is attributed to the cumulative impacts of destructive dredging, environmental stressors, and lost stakeholder support. By reconstructing past baselines and socio-cultural connections, this research identifies important lessons and insights for current shellfish management strategies as we advance to seascape-orientated restoration practices.