temporal variation in seawater temperature plays a crucial role in coral reef ecology. nanwan Bay, Southern taiwan is home to well-developed coral reefs, which frequently experience cold-water intrusions caused by internal wave-induced upwelling, that manifest in distinct daily temperature minima. these temperature minima and their associated sources were studied by recording in situ bottom temperatures and sea levels observed at depths of 5 and 30 m from May 2007 to September 2008. These data were then compared to the East Asian Seas Nowcast/Forecast System, and it was found that daily temperature minima presented large variations with magnitudes of 2-3 °C over periods from days to months. it was further demonstrated that the cold-water intrusions may have originated from depths of ~100 m and were strongly affected by westward propagating mesoscale eddies from the Pacific basin. An impinging warm anticyclonic eddy in July 2007 may have combined with the El Niño, resulting in temperatures surpassing 29 °C and degree heating days >4.0 °C-days at both depths, which were coincidental with a mass coral bleaching event. this eddy's impact was additionally evident in high correlations between daily temperature minima and residual sea levels, suggesting that mesoscale eddies alter stratification, substantially influence temperature variation, and play important roles in understanding ecological processes on coral reefs. Marine environmental conditions vary on multiple temporal scales, and under the influence of climate change, these conditions are likely to change in frequency and magnitude. Seawater temperature is a crucial environmental factor in determining drivers of coral physiology and coral reef ecology 1-4. Mass coral bleaching and mortality, caused predominately by abnormally warm events 5-7 and sometimes by anomalously cold ones 8,9 , highlight the importance of understanding and forecasting seawater temperature variations and extremes 10-12. The effect of seasonal and monthly (lunar) variations in seawater temperature on coral reef ecosystems is well recognized 13 , yet temporal variation on a daily to weekly or shorter scales is rarely studied 7. This is unfortunate given that corals exposed to large daily temperature fluctuations may possess elevated thermal tolerance 12,14. The risk of coral bleaching may also be reduced by high-frequency temperature variability 12. The largest temperature fluctuations in coral reefs are often associated with intermittent upwelling induced by internal waves 7,12,13. Since upwelled cold water has the capacity to act as a buffer from thermal stress during abnormally warm events, these reefs may become refuges in a warming ocean 14-17. Corals inhabiting intermittent upwelling environments have shown a variety of benefits, ranging from improved growth 18 and energy reserves 19 , to enhanced metabolic plasticity 20 , and site-specific physiological acclimatization 21,22. Yet, the influence of mesoscale eddies on corals in these dynamic environments remains unclear 23,24. Fringi...