Elevated nutrients decrease the healthy status of coral communities, which can be stressful on reef corals, always resulting in decreased live scleractinian coral cover (LSCC). Here, we tested the relationship between benthic communities (scleractinian coral, macroalgae, and soft coral) and corresponding environmental parameters to illustrate the current state and potential threats of coral communities in Dongshan, Southern China. These stations were influenced to varying degrees by nutrient enrichment due to severe anthropogenic pressures. Both correlation and regression analysis indicated that increasing concentration of nitrate, nitrite and dissolved inorganic phosphate (DIP) was adversely correlated with LSCC. Conversely, a positive relationship between LSCC and aragonite saturation state (Ω_arag) in the field was also confirmed. Moreover, when the regression models incorporated historical data, potential nutrient tolerance thresholds of the scleractinian coral in Dongshan were identified across the evidences of sharply LSCC decreasing (∼ 2.3 μM for nitrate, ∼ 0.2 μM for nitrite, and ∼ 0.15 μM for DIP). This work demonstrates the environmental parameters varied under frequent anthropogenic disturbances, which in our case shaped LSCC in a potential future reef “refuge” for tropical scleractinian corals. We also confirm the forms-dependent effects of nitrogen on LSCC in a eutrophic environment, suggesting that proper management of reef associated waters, and interpretation of nutrient tolerance thresholds in coral may take nitrogen forms into consideration.