King Harbor in the City of Redondo Beach, California was the site of massive fish kills during 2005 following intense and prolonged red tide events. Weekly monitoring since early 2006 revealed the presence of an abundant and diverse community of potentially harmful dinoflagellate and raphidophyte species in the harbor with highly heterogeneous spatial and temporal distributions. Vertical migration and photoacclimation of dinoflagellates and raphidophytes were investigated as mechanisms for dealing with changing light levels in the King Harbor marina over a 24-hour cycle on 19-20 June 2007. PAR, CTD, chlorophyll fluorescence, dissolved oxygen concentrations, active chlorophyll fluorescence, backscattering, and light absorption and attenuation data were measured every four hours using sensor arrays. Discrete water samples were analyzed for pigment concentrations, particulate and dissolved inorganic nutrients, and phytoplankton community composition using both microscopical and molecular techniques. The overall phytoplankton community composition changed significantly during the 24-hour cycle, and the depth of the chlorophyll maximum moved from shallow waters to deeper depths, and possibly all the way to the sediment interface, during the evening hours. These data suggest a high degree of small-scale heterogeneity in vertical distribution of harmful algal populations and provide important insights into mechanisms that impact community composition within red tide assemblages in King Harbor.