Harmful Algal Blooms (HABs) in Southern California have become recurring events with impacts that surpass the realm of ocean ecosystems. Phytoplankton blooms are natural phenomena, and the same environmental forcings that drive changes in primary productivity and nutrient cycling in the coastal ocean will promote HABs too, including human influences. Therefore, to predict the initiation of HABs, one must define the specific environmental, chemical, and physical parameters that allow the success of the specific species. Recently developed tools and techniques for real-time coastal observing systems allow us to observe dynamics of the coastal ocean on the appropriate spatial and temporal scales, to explore the dynamics of the coastal ocean, to monitor the nutrient loadings, and to follow the development of the HABs. Field studies conducted during 2005 confirmed that observed the transition from the diatom dominated spring to the dinoflagellate dominated summer, both in surface and subsurface waters, was dependent on natural processes affecting the coastal ocean. Lingulodinium polyedrum, our model organism, was present with bloom abundances (~10⁵ cells L^-1) found during the summer, concurrent with low temperature episodes nearshore. Historical temperature record analysis supports our findings on the occurrence of cool temperature anomalies during L. polyedrum blooms in the Southern California Bight, and infer primary controls of temperature, mixed layer depth, and nutrient availability for bloom formation. Using optical instruments deployed on Slocum gliders, we managed to follow the outfall plume, to differentiate it from the natural occurring water masses in the coastal ocean, and to calculate suspended particulate material concentration within the plume. No interaction was found between the nutrient rich plume water and the phytoplankton community. Optical tools were further used in development of red tide spectral indices based on L. polyedrum inherent optical properties. These indices proved to be a successful tool for detection of L. polyedrum blooms in this area, both for in situ absorption and for mooring collected hyperspectral remote sensing reflectance datasets.