Coral reefs are facing rapidly changing environments, but implications for reef ecosystem functioning and important services, such as productivity, are difficult to predict. Comparative investigations on coral reefs that are naturally exposed to differing environmental settings can provide essential information in this context. One prevalent phenomenon regularly introducing alterations in water chemistry into coral reefs are internal waves. This study therefore investigates the effect of large amplitude internal waves (LAIW) on primary productivity in coral reefs at the Similan Islands (Andaman Sea, Thailand). The LAIW-exposed west sides of the islands are subjected to sudden drops in water temperature accompanied by enhanced inorganic nutrient concentrations compared to the sheltered east. At the central island, Ko Miang, east and west reefs are only few hundred meters apart, but feature pronounced differences. On the west lower live coral cover (-38 %) coincides with higher turf algae cover (+64 %) and growth (+54 %) compared to the east side. Turf algae and the reef sand-associated microphytobenthos displayed similar chlorophyll a contents on both island sides, but under LAIW exposure, turf algae exhibited higher net photosynthesis (+23 %), whereas the microphytobenthos displayed reduced net and gross photosynthesis (-19 % and -26 %, respectively) accompanied by lower respiration (-42 %). In contrast, the predominant coral Porites lutea showed higher chlorophyll a tissues contents (+42 %) on the LAIW-exposed west in response to lower light availability and higher inorganic nutrient concentrations, but net photosynthesis was comparable for both sides. Turf algae were the major primary producers on the west side, whereas microphytobenthos dominated on the east. The overall primary production rate (comprising all main benthic primary producers) was similar on both island sides, which indicates high primary production variability under different environmental conditions.