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The coral species Siderastrea stellata Verril 1868 is endemic and common in Brazil. This species is a colonial, massive, zooxanthellate coral and one of the most important reef builders in many reef areas. The photosynthetic symbionts are very sensitive to environmental variations, such as sedimentation and temperature variations, which can disturb the complex interaction between the animal host and endosymbiont. In this study, we simulated the conditions found in the field in a series of experiments that evaluated chlorophyll a fluorescence emissions. Chlorophyll a maximum quantum yield and Rapid Light Curves (RLCs) were generated using a red light pulse amplitude modulated fluorometer, Mini-PAM, in S. stellata colonies under different irradiance, temperature and burial levels. Moreover, the PSII fluorescence yield was tested using a chlorophyll a fluorescence spatial detection method, which was implemented for the first time using an imaging system for S. stellata coral species. S. stellata showed great adaptive capacity under different light regimes between 50 and 160 mu mol photons m(-2) s(-1). When a moderate burial level factor was analyzed synergistically with temperatures below 18 degrees C, we observed resilient colonies. However, at critical burial levels and high temperatures (28 degrees C) after 10 days, lower maximum quantum yields of PSII chlorophyll a fluorescence were detected, exhibiting an abrupt decrease after 96 h of burial. Continuous evaluations of coral environments and a strong understanding coral ecophysiology are extremely important for the establishment of minimum health risk levels for coral reef environments and coastal management measures. We conclude that ecophysiological aspects are highly specific and should be evaluated according to the preconditions of organism acclimatization. The chlorophyll a fluorescence imaging technique was shown to be an efficient tool for evaluating the physiologic status of zooxanthellae over the surface of a coral such as S. stellata. In turn, the photobiology results indicated the life history of this species in the upwelling waters of the region, as this species had higher Fv/Fm values at lower temperatures and intermediary burial conditions than at higher temperatures.