Oyster reefs are critically endangered coastal habitats which provide valuable ecosystems services. Despite their importance, there remains a significant knowledge gap in our understanding of how oyster and sediment characteristics influence the ecological functioning and biodiversity of remnant Australian flat oyster (Ostrea angasi) reefs. To inform restoration efforts, we assessed relationships between community respiration rates (CR), inorganic nitrogen fluxes, filtration rates, biodiversity, and oyster morphometrics as well as sediment conditions for three remanent flat oyster reefs (Oyster Cove, Ralphs Bay, and Quarantine Bay) in southeast Tasmania. Additionally, we explored relationships between net denitrification, and flat oyster morphometrics and sediment conditions at one of the sites (Ralphs Bay) in southeast Tasmania. We observed positive relationships between CR, inorganic nitrogen fluxes, filtration rates, and live flat oyster biomass, as well as between the richness and biomass of associated taxa and total flat oyster biomass (both tissue and shell including dead shell), across all three locations. We also found an increase in net denitrification associated with live oyster biomass at one of the oyster reefs (Ralphs Bay). The CR, inorganic nitrogen fluxes, filtration rates, diversity of taxa and biomass of bivalves and flat oyster biomass was higher at Ralphs Bay, which has the most intact reef, compared to the other two locations. In contrast to other studies, the organic and silt content of the sediment showed limited influence on CR, inorganic nitrogen fluxes, filtration rates and net denitrification. CR, and inorganic nitrogen fluxes in these flat oyster reefs were like other restored and natural oyster reefs globally, but net denitrification, filtration rate and taxonomic richness exceeded those previously observed globally. These results highlight the important role of oyster biomass in enhancing water quality and biodiversity. Burgeoning flat oyster reef restoration initiatives should prioritise the enhancement of both live oyster populations and dead shells to recover their associated ecological functions and biological diversity.