Observations of coral reef losses to climate change far exceed our understanding of historical degradation before anthropogenic warming. This is a critical gap to fill as conservation efforts simultaneously work to reverse climate change while restoring coral reef diversity and function. Here, we focused on southern China’s Greater Bay Area, where coral communities persist despite centuries of coral mining, fishing, dredging, development, and pollution. We compared subfossil assemblages with modern-day communities and revealed a 40% decrease in generic diversity, concomitant to a shift from competitive to stress-tolerant species dominance since the mid-Holocene. Regions with characteristically poor water quality—high chl-a, dissolved inorganic nitrogen, and turbidity—had lower contemporary diversity and the greatest community composition shift observed in the past, driven by the near extirpation of Acropora. These observations highlight the urgent need to mitigate local stressors from development in concert with curbing greenhouse gas emissions.