Variability in the physical ocean environment affects the northern California shelf, and defines the environmental setting. The California Current is an eastern boundary surface current that flows toward the equator and affects the physical oceanographic conditions along the west coast and northern California shelf. Inshore of the California Current, the Davidson current flows toward the equator along the coast in the spring/summer, and seasonally reverses, flowing pole-ward along the coast in the winter. North Pacific waters feeding the California Current are generally low salinity and temperature, with high oxygen and nutrients. The spatial-temporal variability of the California Current affects the continental shelf and the marine biota along the west coast.

North winds blowing in spring and summer result in upwelling of cold, deep water with low oxygen and high nutrients onto the shelf. The upwelling strength is based on wind strengths and strongly affects productivity and food webs on the shelf. The transition from winter/southwesterly winds to spring/northerly winds that result in upwelling is references as the Spring Transition, which can occur between March and June. The earlier in the year that the Spring Transition occurs, the greater the productivity in coastal waters. Variability associated with upwelling is greater across the shelf and can result in hypoxic waters impinging shallow shelf habitats, as observed off large sections of the Oregon shelf in 2002 and 2006.