Seasonal anomalies of salinity, phytoplankton chlorophyll a, and zooplankton volume off Baja California were examined from data obtained during 2001-2007. The analyses helped to identify a strong effect of physical processes on the pelagic ecosystem, diminishing near surface salinity and water column integrated phytoplankton biomass, and enhancing zooplankton volume. These changes are associated with an increase of the Pacific Decadal Oscillation (PDO) index, characterizing a warm phase of the index from summer 2002 to at least summer 2006. Negative chlorophyll a anomalies appear to respond to zooplankton grazing activity, with a possible "top down" effect during this period. Empirical orthogonal functions (EOFs) of Ekman drift reveal the seasonal and interannual patterns that describe the influence of upwelling zones, and there was a strong response to changes in the equatorward wind forcing from 2002 to 2006. The relationship between negative salinity anomalies and the two ternporal EOF modes of Ekman drift was evident as a result of relaxation of coastal upwelling during this period. After 2006, the PDO index showed more neutral or negative values, defining the beginning of a cool phase, with positive near-surface salinity anomalies off Baja California.