Nitrogen isotopic compositions of zooplankton in the California Current Ecosystem (CCE) are known to vary over inter‐annual scales of climate variability, but the extent to which those changes are driven by variations in baseline phytoplankton δ¹⁵N values vs. zooplankton trophic position (TP) is poorly resolved. We use field samples collected during a large natural environmental perturbation, the 1998–1999 alternation between El Niño and La Niña states, to test the ability of large dominant CCE zooplankton Euphausia pacifica and Calanus pacificus to alter their TPs in response to environmental variability. To distinguish trophic changes from variations of δ¹⁵N values at the base of the food web, the zooplankton were assayed by Compound Specific Isotope Analysis of Amino Acids (CSIA‐AA). Linear mixed‐effect models were developed to utilize data from all amino acids (AAs), providing greater statistical power than the typical CSIA‐AA approach of using only phenylalanine and glutamic acid. We confirm a significant ¹⁵N enrichment of ∼ 2‰ at the base of the food web for all AAs and all zooplankton groups during the 1998 El Niño. This baseline enrichment in ¹⁵N has been speculated to occur during El Niño events but never conclusively shown. We also demonstrate a significantly elevated TP, implying increased carnivory during 1998, for E. pacifica while C. pacificus did not alter their TP between years. Lastly, TPs calculated from the standard CSIA‐AA equation with laboratory‐derived constants gave unrealistically low estimates, suggesting an assessment of these variables in situ is needed for an accurate application in natural systems.