Abstract: Coral bleaching and mortality events have recently increased in frequency and severity in the whole world. Combined effects of natural and anthropogenic impacts were assumed to be the cause for coral’s health degradation. Sedimentation, urban waste, sewage discharge and agricultural activities are among the nutrient input for Malaysian waters, which can affect the coral reefs indirectly. In this study, photosynthetic performance of tropical corals under stresses were studied by exposing three common tropical scleractinian corals, Stylophora pistillata, Montipora digitata and Seriatopora hystrix to combination of different levels of high and ambient temperature and in a laboratory condition. Quantum yield fluorescence before, after stress and after recovery stage were recorded using a dark-adapted photochemical efficiency (Fv/Fm) methodology with a pulse-amplitude-modulation (PAM) chlorophyll fluorometer (WATER-PAM, Walz, Germany). Physical appearance of the corals were after the post-stress stages. The results showed that nutrient enrichment not have a synergistic effect, and that high temperatures alone significantly impact Fv/Fm values (three-way ANOVA, p > 0.05) for all coral species. Slow growing corals (S. pistillata) appeared to cope better with the high temperatures than the fast-growing corals (M. digitata and S. hystrix). Hence, that a nitrate concentration contributed as an intial response of the symbiont’s physiological changes, which can give more understanding on studying specific coral species resistance towards coral bleaching issues.