Eastern boundary current systems are among the most productive and lucrative ecosystems on Earth because they benefit from upwelling currents. Upwelling currents subsidize the base of the coastal food web by bringing deep, cold and nutrient-rich water to the surface. As upwelling is driven by large-scale atmospheric patterns, global climate change has the potential to affect a wide range of significant ecological processes through changes in water chemistry, water temperature, and the transport processes that influence species dispersal and recruitment. We examined long-term trends in the frequency, duration, and strength of continuous upwelling events for the Oregon and California regions of the California Current System in the eastern Pacific Ocean. We then associated event-scale upwelling with up to 21 years of barnacle and mussel recruitment, and water temperature data measured at rocky intertidal field sites along the Oregon coast. Our analyses suggest that upwelling events are changing in ways that are consistent with climate change predictions: upwelling events are becoming less frequent, stronger, and longer in duration. In addition, upwelling events have a quasi-instantaneous and cumulative effect on rocky intertidal water temperatures, with longer events leading to colder temperatures. Longer, more persistent upwelling events were negatively associated with barnacle recruitment but positively associated with mussel recruitment. However, since barnacles facilitate mussel recruitment by providing attachment sites, increased upwelling persistence could have indirect negative impacts on mussel populations. Overall, our results indicate that changes in coastal upwelling that are consistent with climate change predictions are altering the tempo and the mode of environmental forcing in near-shore ecosystems, with potentially severe and discontinuous ramifications for ecosystem structure and functioning.