To explore potential acclimatization mechanisms of reef corals to the frequent and intense disturbances caused by Large Amplitude Internal Waves (LAIW), the prey capture disposition and photosynthetic performance (Fv/Fm) of corals were investigated in relation to changes in the water temperature, pH, flow speed and food availability. LAIW simulation studies were carried out under controlled laboratory conditions using Porites lutea as a model organism. Cold water stress caused an immediate retraction of the coral polyps into their calyxes, particularly when also the pH was altered, whereas the pH alone caused the expansion of the polyps. Moreover, the life history of the colonies played a crucial role in their responses, where corals previously exposed to LAIW in the field showed lower retraction levels than LAIW-inexperienced controls, suggesting acclimatization. Although the presence of food stimulated polyp expansion, we found an overriding effect of the thermal stress causing polyp contraction. Low temperature did not seem to influence the photosynthetic yield, but LAIW-experienced corals showed higher performance than LAIW-inexperienced controls and were able to sustain those high levels in long term experiments, relative to the controls. This study suggests that LAIW invoke phenotypic acclimations which may be important in strengthening their metabolic performance and resistance to stressors at different scales.