The West Antarctic Peninsula region is an important source of Antarctic krill (Euphausia superba) in the Southern Ocean. From 1980–2004 abundance and concentration of phytoplankton and zooplankton, krill reproductive and recruitment success and seasonal sea ice extent here were significantly correlated with the atmospheric Southern Oscillation Index and exhibited three- to five-year frequencies characteristic of El Niño–Southern Oscillation (ENSO) variability. This linkage was associated with movements of the Southern Antarctic Circumpolar Current Front and Boundary, a changing influence of Antarctic Circumpolar Current and Weddell Sea waters, and eastward versus westward flow and mixing processes that are consistent with forcing by the Antarctic Dipole high-latitude climate mode. Identification of hydrographic processes underlying ecosystem variability presented here were derived primarily from multi-disciplinary data collected during 1990–2004, a period with relatively stable year-to-year sea ice conditions. These results differ from the overwhelming importance of seasonal sea ice development previously established using 1980–1996 data, a period marked by a major decrease in sea ice from the Antarctic Peninsula region in the late 1980s. These newer results reveal the more subtle consequences of ENSO variability on biological responses. They highlight the necessity of internally consistent long-term multidisciplinary datasets for understanding ecosystem variability and ultimately for establishing well-founded ecosystem management. Furthermore, natural environmental variability associated with interannual- and decadal-scale changes in ENSO forcing must be considered when assessing impacts of climate warming in the Antarctic Peninsula–Weddell Sea region.