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Abstract The growing coastal development, dredging and dumping activities, overfishing and expansion of marine cage culture in Nha Trang Bay ( NTB ) of Central Vietnam since the beginning of the 2000s have resulted in a dramatic decrease of live coral cover. Surveys conducted in April–May 2013 and the same period in 2014 revealed that with an increase in distance from the outer part of the bay towards the mainland, the rivers’ influxes and dredged areas, coral cover decreased from 75% to 0.6% and species richness from 63 to 5, while the abundance of macroalgae increased from 0% to 56%. These changes correlate with differences in the concentration of suspended sediments on the same gradient. The abundance of the crown‐of‐thorns starfish Acanthaster planci and of the echinoid Diadema setosum significantly increased between the first estimation in 1998 and the survey in 2014, from 0 to 1.7 individuals (ind.) per 100 m −2 and from 50.8 to 94.5 ind. per 100 m −2 , respectively, contributing to coral loss and intensive bioerosion of the reef framework in the bay. The large sizes of adult colonies of tabulate Acropora on the remote stations with negligible sedimentation and eutrophication loads were inconsistent with the assumptions that temperature‐induced coral bleaching or cyclones could be the major impacts in Nha Trang Bay. Analysis of the 16‐year thermal history of the bay did not reveal any instances in which the coral thermal bleaching threshold had been exceeded up to the present study. Seasonal upwelling, which occurs annually in the vicinity of Central Vietnam, may contribute to mitigation of thermal anomalies within NTB and to the maintenance of healthy coral communities on the remote reefs with relatively low anthropogenic impact.