During spring and summer time, coastal upwelling influences circulation and ecosystem dynamics of the Monterey Bay, California, which is recognized as a National Marine Sanctuary. Observations of physical, bio‐optical properties (including bioluminescence) together with results from dynamical biochemical and bioluminescence models are used to interpret the development of the upwelling event during August 2003 in Monterey Bay, California. Observations and the biochemical model show the development of a phytoplankton bloom in the southern portion of Monterey Bay. Model results show an increase of nutrients in the southern portion of the bay, where nutrient‐rich water masses are brought in by the southward flow and cyclonic circulation inside the bay. This increase in nutrients together with the sluggish circulation in the southern portion of the bay provides favorable conditions for phytoplankton growth. Our observations and models suggest that with the development of upwelling the offshore water masses with the subsurface layer of bioluminescent zooplankton were replaced by water masses advected from the northern coast of the bay with a relatively high presence of mostly nonbioluminescent phytoplankton. Inshore observations from autonomous underwater vehicles (AUVs) show consistent coincidence of chlorophyll, backscatter, and bioluminescence maxima during upwellingdevelopment. Offshore AUV observations (taken at the entrance to the bay) show a deeper bioluminescence maximum below the surface layers of high chlorophyll and backscatter values during the earlier stages of upwelling development. Later, the observed deep offshore bioluminescence maximum disappeared and became a shallower and much weaker signal, coinciding with high chlorophyll and backscatter values offshore. Based on the biochemical and bioluminescence models, a methodology for estimating the nighttime water leaving radiance due to stimulated bioluminescence is demonstrated and evaluated.



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