Increasing ocean temperatures due to global warming are predicted to have negative effects on coral reef fishes. El Niño events are associated with elevated water temperatures at large spatial (1000s of km) and temporal (annual) scales, providing environmental conditions that enable temperature effects on reef fishes to be tested directly. We compared remote sensing data of sea surface temperature (SST) anomalies, surface current flow and chlorophyll-a (Chl-a) concentration with monthly patterns in larval supply of coral reef fishes in nearshore waters around Rangiroa Atoll (French Polynesia) from January 1996 to March 2000. This time included an intense El Niño (April 1997–May 1998) event between two periods of La Niña (January–March 1996 and August 1998–March 2000) conditions. There was a strong relationship between the timing of the El Niño event, current flow, ocean productivity (as measured by Chl-a) and larval supply. In the warm conditions of the event, there was an increase in the SST anomaly index up to 3.5 °C above mean values and a decrease in the strength of the westward surface current toward the reef. These conditions coincided with low concentrations of Chl-a (mean: 0.06 mg m−3, SE ± 0.004) and a 51% decline in larval supply from mean values. Conversely, during strong La Niña conditions when SST anomalies were almost 2 °C below mean values and there was a strong westward surface current, Chl-a concentration was 150% greater than mean values and larval supply was 249% greater. A lag in larval supply suggested that productivity maybe affecting both the production of larvae by adults and larval survival. Our results suggest that warming temperatures in the world's oceans will have negative effects on the reproduction of reef fishes and survival of their larvae within the plankton, ultimately impacting on the replenishment of benthic populations.