This study was conducted in Esquimalt lagoon, located southwest of Victoria, British Columbia, Canada. Physical characteristics of the water column, e.g. circulation and stratification, changed seasonally resulting from variations in tides, temperature, precipitation and wind. Chemical characteristics, e.g. oxygen and dissolved nutrient concentrations, also differed temporally relative to those in the lagoon’s ocean source water (Juan de Fuca Strait) because of variations in local photosynthesis and nutrient use by phytoplankton. Diatom blooms occurred in the spring, and blooms of photosynthetic flagellates (Heterosigma akashiwo (2009) and Akashiwo sanguinea (2009 and 2010)) occurred in the late summer and early fall when nitrate, ammonium, and urea were depleted. Proliferation of these flagellates led to the development of harmful algal blooms (HABs) associated with oxygen depletion in the lagoon bottom waters. Increased oxygen demand from bacterial degradation of algal biomass and exudates was the likely cause for bottom water hypoxia under reduced tidal exchange. / Graduate