Abstract Non‐stationarity (time‐varying mean or variance) in climate conditions can alter relationships between basin‐scale climate indices and the ecological conditions that map onto them. We consider evidence of time‐varying climate conditions in the California Current System (CCS) based on sea level pressure dynamics that characterize the North Pacific High (NPH), and evaluate the temporal stability of regional relationships between climate indices and physical and biological conditions across the CCS. We find relationships between climate indices and ecological conditions are relatively stable through time, but do not capture short‐term ecological trends. These results show that popular basin‐scale climate indices are insufficient in characterizing the North Pacific climate system, especially from ecosystem perspectives. Applications of associations between climate and ecological variables should consider proximate physical forcing mechanisms and the stability of relationships through time.