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Intensive sampling in coastal waters of the central Red Sea during a period of thermal stratification showed that vertical patches of prokaryotes and nano- and microplankton developed and persisted for at least a week within the apparently well mixed layer. This vertical structure was most likely the result of in situ growth and mortality (e.g., grazing) rather than physical or behavioral aggregation. Adding nutrient-rich deep water simulating a mixing event triggered dense phytoplankton blooms in this nutrient-poor environment. These findings have implications for present bloom-forming theories because suggest that vertical structure within the mixed layer provides a critical seed mass that can rapidly exploit nutrient influx during early seasonal mixing.