Intense El Niño events severely impact seabird populations, often months in advance of peak temperature anomalies. The trophic mechanisms responsible for these impacts are unknown but are assumed to operate at seasonal scales and to be linked to ocean productivity changes. Precursors to El Niño events include changes in both sea-surface temperature and the depth of the 20 degrees C thermocline. Foraging piscivorous seabirds are known to be sensitive to both thermocline depth and sea-surface temperature change, but the potential influence of these phenomena on breeding dynamics is unknown. Using 18 years of data on three seabirds of the western tropical Pacific, we show that pelagic seabird breeding participation is directly and independently related to changes in both surface chlorophyll concentration and thermocline depth that occur well in advance of El Niño generated sea-surface temperature anomalies. In contrast, breeding in an inshore foraging species is not correlated with any environmental/biological parameters investigated. These findings demonstrate that El Niño related phenomena do not affect seabird prey dynamics solely via productivity shifts at seasonal scales, nor in similar ways across different seabird foraging guilds. Our results also suggest that population declines observed in the western tropical Pacific may be directly related to the frequency and intensity of El Niño anomalies over the study period.