Oyster reefs are one of the most degraded marine habitats, with at least 85% lost globally, likely an underestimate in the highly developed coastlines of Asia. Oyster reefs in Hong Kong, for example, have now been assessed as a Critically Endangered ecosystem. Hong Kong’s western waters suffer from extremely high levels of nitrogen inputs from the Pearl River Estuary, which houses a population of over 80 million people. Even in heavily degraded states oyster habitats amplify denitrification, but demonstrating the magnitude of this service is key to understanding the benefits of restoration. Therefore, to understand the current and potential future capacity of denitrification by oyster reefs in Hong Kong, we quantified denitrification by both intertidal and subtidal oyster and adjacent soft-sediment habitats at multiple locations across different seasons. We found that mixed-species oyster habitat (primarily Magallana spp.) in the intertidal and subtidal waters increased denitrification by >19 and >82 times greater than the bare soft-sediment, respectively. These rates varied by season, with denitrification rates being much higher in summer, likely a response to temperature. Therefore, while oyster reefs in Hong Kong have been exploited to near functional extinction, our data show that large-scale restoration would substantially benefit the quality of coastal waters through the high filtration and denitrification capacity of the native oysters in the region.