Analysis of monthly coastal upwelling intensities revealed two seasonal and biologically relevant upwelling ‘modes’ in the California Current Ecosystem (CCE). The first mode reflected upwelling during the summer months and was characterized by low-frequency (multidecadal) processes, including significant (P<0.01) linear trends at some latitudes. In contrast, the second mode reflected wintertime upwelling and was defined by higher-frequency variability associated with the North Pacific High and El Niño Southern Oscillation events. These modes were compared with multidecadal time series of splitnose rockfish (Sebastes diploproa) otolith growth, yelloweye rockfish (S. ruberrimus) otolith growth, Chinook salmon (Oncorhynchus tshawytscha) scale growth, and indices of Cassin's auklet (Ptychoramphus aleuticus) and common murre (Uria aalge) reproduction in the central-northern CCE. In redundancy and correlation analyses, salmon growth and Cassin's auklet fledgling success associated with the summer upwelling mode while all other time series associated with the winter upwelling mode, indicating that CCE biology was differentially sensitive to these seasonal upwelling patterns. Thus, upwelling occurred in unrelated seasonal modes with contrasting trends, atmospheric forcing mechanisms, and impacts on the biology of the CCE, underscoring the importance of seasonality when evaluating ecosystem response to climate variability and change.