Field measurements at Dongsha Atoll in the northern South China Sea showed frequent drops in daily water temperature up to 8°C during intrusions of large nonlinear internal waves. The internal waves had a period of about 4 hours and velocity amplitude of 0.3 m s−1. Large variations of dissolved oxygen were observed a week after cold-water intrusion, which was followed in another 2 days by a significant increase of chlorophyll content. The 7–8-day delay suggests that phytoplankton blooms occurred after the nutrients were released through microbial decomposition of organics brought up by the internal waves. This study highlights the effects of internal waves and the possible role of the microbial food web on nutrient regeneration in a tropical reef ecosystem.