Coastal upwelling regions represent less than 2% of the marine biosphere's volume. Nonetheless, local biogeochemical processes have a considerable impact on the structure and functioning of the global oceans. In this study we characterize the evolution of biogeochemical properties during the upwelling seasons of 2009 and 2010 in the coastal ecosystem off central Oregon (west coast of USA). Both years displayed similar cumulative upwelling favorable winds and total input of preformed nutrients into the midshelf despite of their marked differences in the timing of the onset of the upwelling season, its duration and the number of upwelling relaxation events. However, these differences in upwelling forcing induced inter-annual variability in oxygen and nitrogen deficiencies, particulate matter accumulation and nutrient regeneration. Our results suggest that the summer evolution of nitrogen loss and oxygen depletion over the shelf does not follow a simple relationship with the cumulative upwelling index. We hypothesize that other factors, such as the intensity and persistence of the upwelling, which affect the residence time of water masses over the continental shelf, play a key role in the cumulative effect of biological processes leading to hypoxia in these coastal environments.