Oceanographic conditions in the Pacific waters off Baja California are described for the period 2002–2003. Anomalies in the temperature-salinity relationships were observed from October 2002 to April 2003, with a clear contribution of low salinity and low temperature subarctic water in the upper 100 m of the water column. Below 100 m, physical data suggested weak El Niño conditions. Weakened or poleward winds were not observed. The pelagic ecosystem during the intrusion of subarctic waters showed strong seasonal changes, with localized centers of high chlorophyll and zooplankton in July 2002, followed by a strong decrease in the following autumn and winter seasons. Both chlorophyll and zooplankton rebounded in April 2003, but zooplankton showed a stronger onshore-offshore gradient. There was no strong biological signal. The zooplankton taxa that showed an increase during El Niño 2002-2003 were salps and chaetognaths. The increase of salps did not appear to be related to this event, due to their seasonal occurrence limited to the northern region. In contrast the increase of chaetognaths presented a similar pattern to that observed in El Niño 1997-1998.