In thermodynamic equilibrium with sea water the Sr/Ca ratio of aragonite varies predictably with temperature and the Sr/Ca ratio in coral have thus become a frequently used proxy for past Sea Surface Temperature (SST). However, biological effects can offset the Sr/Ca ratio from its equilibrium value. We report high spatial resolution ion microprobe analyses of well defined skeletal elements in the reef-building coral Porites lutea that reveal distinct monthly oscillations in the Sr/Ca ratio, with an amplitude in excess of ten percent. The extreme Sr/Ca variations, which we propose result from metabolic changes synchronous with the lunar cycle, introduce variability in Sr/Ca measurements based on conventional sampling techniques well beyond the analytical precision. These variations can limit the accuracy of Sr/Ca paleothermometry by conventional sampling techniques to about 2degreesC. Our results may help explain the notorious difficulties involved in obtaining an accurate and consistent calibration of the Sr/Ca vs. SST relationship.