To realize the specific-time importance of phytoplankton variability in the semi-enclosed marine basin (Eastern Harbour of Alexandria), the present study based on a short-time scale was conducted during a year cycle. The harbour is characterized by abrupt temporal variations of multitudes of different environmental variables and experiences a high degree of pressure from natural and anthropogenic activity. The instability of the system and rapid phytoplankton variations hinder the full understanding of the mechanism that underlying the differences in the community composition and production. The community structure responded quickly to modifications, consequently, displacement of different species occur in a couple of days. The study stresses the crucial role of temperature as a steering factor in determining the timing, magnitude, and composition of the spring bloom. Water mixing conditions and organic matter concentrations influence deeply the phytoplankton variability. The study examines the ecology of the massive blooms of potentially harmful/toxic species of different classes.