This study aimed to investigate the effects of the heavy metals, copper, zinc and lead, on the photo-physiology of the symbiotic dinoflagellate Symbiodinium isolated from the coral Fungia repanda. Freshly isolated Symbiodinium found to belong to clade C were exposed to different concentrations of the three heavy metals for 3-hour and 18-hour treatments at 28°C and 32°C. The Pulse Amplitude Modulated (PAM) fluorometry technique was used to determine the maximum quantum yield (Fv/Fm), relative maximum electron transport rate (rETRmax) and maximum non-photochemical quenching (NPQmax) of the photosystem II (PSII). An increase in non-photochemical quenching accompanied by a decrease in photosynthetic capacity was noted for copper at a concentration of 50 µg/L for both temperatures. The Fv/Fm was not significantly affected by the Zn treatments. However, at 28 °C, isolates treated with 100 µg/L Zn for 18 hours showed an increase in non-photochemical quenching accompanied by a decrease in photosynthetic capacity. Pb had the most profound effect on all of the isolates. The Fv/Fm significantly decreased and an increase in NPQmax was noted. The decrease of rETRmax and increase in NPQmax for the heavy metal bioassays under 32 °C were more significant than at 28 °C. This study suggests that Cu (≥50 µg/L), Zn (≥ 100 µg/L) and Pb decrease the photosynthetic capacity of the Symbiodinium isolates from F. repanda especially more so with increasing temperatures.