Increasing temperatures on a global scale and locally deteriorating water quality affect coral distribution and health. Mechanisms that convey environmental robustness are poorly understood and have been attributed to the coral host, algal symbionts, and prokaryotic associates. Flexibility of the host’s (bacterial) microbiome has been suggested to contribute to environmental robustness, but the underlying mechanisms are unclear. We therefore utilised the vastly contrasting water quality gradient present along Hong Kong’s highly urbanised coastline to explore whether flexibility in the microbiome of Oulastrea crispata relates to spatial variations in temperature, salinity, dissolved oxygen, pH, nitrate, nitrite, ammonia, total nitrogen, phosphorus, turbidity, and chlorophyll a. We identified differences in the coral microbiomes between sites, but the measured environmental variables only explained ~ 23% of the variation suggesting other factors are contributing substantially. The observed structural complexity of the microbiome (based on alpha diversity indices) appears to be relatively conserved across the environmental gradient even at sites where no other hard coral can survive. Therefore, we conclude that, at least in O. crispata, flexibility in the microbiome does not appear to underpin the robustness of this broadly distributed coral.