Phytoplankton biomass in the northern Humboldt Current system is known to fluctuate over intra- and interannual time scales in response to environmental variability. General changes in the phytoplankton community are known, but a quantitative description of the link between environmental signals and observed changes is lacking. The present study examines these links through an analysis of long-term phytoplankton community changes in Ancon Bay, Peru (118S) from 1992 to 2004. The correlation of several environmental signals with phytoplankton biovolume was explored using stepwise multiple regression and community analyses. Results indicate that environmental signals of interannual periodicity, e.g. those most associated with the El Niño Southern Oscillation, were responsible for overall biovolume levels, while signals of annual periodicity (i.e. sea surface temperature) correlated to changes in phytoplankton taxa proportions. Specifically, diatoms (e.g. Chaetoceros spp., Actinocyclus octonarius and Skeletonema costatum) dominate biovolume only during the coldest periods (13-168C) when upwelling is strongest,whereas dinoflagellates dominate warmer periods. During warm periods, a decrease in offshore transport or the intrusion of offshore waters (e.g. from beyond the shelf ) increases the proportion of later phytoplankton successional stages, within the bay (e.g. dinoflagellates, flagellates and silicoflagellates). These results suggest that cross-shelf interactions between offshore and nearshore habitats exist at both intra- and interannual scales as affected by local upwelling variability, with possible consequences for resources of the nearshore upwelling ecosystem. © The Author 2010.