Conocarpus lancifolius Engl. (Combretaceae), a heat tolerant plant, has potential for use in the phytoremediation of polluted soil. We analyzed the physiological changes in C. lancifolius exposed to single and mixed heavy metals (HMs; cadmium, nickel, and lead). For 30 days under controlled growth conditions, we exposed some groups of plants to a single HM at concentrations of 25 or 50 μmol·L–1 and other groups were exposed to 25 μmol·L–1 of a mixture of HMs. Photosynthetic parameters such as electron transport rate, photosynthetic rate, chlorophyll fluorescence, chlorophyll content index, and photosynthetic pigments were measured. Chloroplast morphology was studied by transmission electron microscopy (TEM). In plants exposed to 25 μmol·L–1 of HMs, the photosynthetic parameters were unaffected, whereas at 50 μmol·L–1 of HMs, all parameters significantly decreased up to 20 days of exposure, followed by an increase up to 30 days, indicating a slow adaptation of plants to HM under stress. Compared with the single HMs, mixtures of HMs were more toxic at the same concentration. All parameters indicated damage to the photosynthetic apparatus due to stress from 25 μmol·L–1 of the HM mixtures and 50 μmol·L–1 of the single HMs. TEM analyses showed a dispersion of grana in the chloroplast of the affected C. lancifolius plants.