Using a database of roughly 300 basin-wide conductivity-temperature-depth (CTD) stations per year from 1997 to 2003, we examined interannual and seasonal variability of nutrients and chlorophyll across the equatorial Pacific. During this period, chlorophyll concentrations exceeded the range of previous measurements for this region. Nitrate, silicic acid, and phosphate also varied widely but not necessarily coherently with each other or with chlorophyll. Across the La Niña to El Niño continuum there was nonmonotonic variability in chlorophyll, particulate backscatter (a proxy for phytoplankton carbon), and large size fraction (diatom) chlorophyll. In general, while El Niño was associated with decreased phytoplankton biomass, there was no corresponding increase in phytoplankton or diatoms during La Niña. However, there were increases in macronutrients in response to La Niña. We suggest that the lack of a biological response to these nutrient increases is due to their decoupling from iron supply. Multiple linear regression analysis of the physical factors responsible for vertical nutrient fluxes emphasized the importance of winds in the central and western Pacific, and thermocline depth in the east. We suggest that the role of the winds is not limited to enhancement of upwelling, but perhaps more importantly to increased vertical mixing of nutrients. Seasonal patterns were weak but consistent with previous work which has suggested that enhanced productivity in the second half of the calendar year causes reduced surface pCO2. Enhanced coverage of nutrient sensors on the tropical atmosphere ocean (TAO) array would help to quantify seasonal signals associated with processes such as tropical instability waves and lead to a better understanding of the links between productivity, carbon export, and air-sea CO2 exchange.