Coral bleaching is the major threat to coral reefs worldwide. Coral reefs, as an essential part of the marine ecosystem, are under severe threat from many sources, including high sea water temperatures, solar irradiance and anthropogenic impacts such as nutrient enrichment, sewage disturbance and others. Malaysian corals were affected during the global mass bleaching events in 1998 and 2010 which caused bleaching and some mortality, but coral reef degradation is also due to other causes. Mostly Peninsular Malaysia coral reefs are affected by agricultural activities and human development causing sedimentation and nutrient runoff. To date, the photosynthetic performance of Malaysian corals under such stresses is unknown, and laboratory experiments were conducted to assess how some commonly occurring corals of that region respond to stress factors. The objectives of this study were: (1) To record maximum quantum yield of chlorophyll fluorescence (Fv/Fm) of coral species; Stylophora pistillata, Montipora digitata and Seriatopora hystrix in treatments of stressors of high/ambient temperature-light levels and high/ambient temperature-nitrate levels, (2) To record maximum quantum yield of chlorophyll fluorescence (Fv/Fm) of coral species in stress treatments of combinations of high/ambient temperature-light levels and high/ambient temperature-nitrate levels, (3) To differentiate changes in quantum yield fluorescence among the three corals species before stress, after stress and after 24-h recovery stage. Colours and paling were also being examined by using CoralWatch Coral Health Chart. To achieve this, S. pistillata, M. digitata and S. hystrix were exposed to: a) ambient (27°C, 200 μmol quanta m⁻²s⁻¹), (b) high light (27ºC, 520 μmol quanta m⁻²s⁻¹), (c) high temperature (30°C, 200 μmol quanta m⁻²s⁻¹) and (d) high temperature + high light (30°C, 520 μmol quanta m⁻²s⁻¹). In a further investigation, the overnutrification factor was introduced: (a) ambient control (27ºC, 2 μM NO3⁻), (b) high nitrate (27ºC, 15 μM NO3⁻), (c) high temperature (30ºC, 2 μM NO3⁻), (d) high temperature + high nitrate (30ºC, 15 μM NO3). 20 minutes of dark-adapted photochemical efficiency (Fv/Fm) was measured using a pulse-amplitude-modulation (PAM) chlorophyll fluorometer (WATERPAM, Walz, Germany). Besides, here it includes the study of Reef Check data and relates it with 50-km monitoring product of Degree Heating Week Coral Reef Watch for 2009 until 2011 in Peninsular Malaysia and East Malaysia to predict bleaching behaviours within Malaysian waters. For the temperature-light stress treatments, there were significant decreases in maximum quantum yield for all species, due to photoinhibition. The results show that S. hystrix is susceptible to thermal stress. In temperature-nitrate stress experiments, it is suggested that nutrient enrichment may 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) appear to cope better with the environmental changes than the fast-growing corals (M. digitata and S. hystrix). This research helps understand the effects of coral bleaching and nitrate stress and may be of value to researchers and managers of marine parks in the Malaysian region to better understand coral health.