Coastal lagoons are biodiversity hotspots that support neighboring ecosystems and various services. They can exhibit distinct biophysical characteristics compared to the adjacent open sea and act paradoxically as autonomous ecosystems. Using remotely sensed observations and state-of-the-art numerical simulations, the role of water column hydrodynamics in shaping the seasonal succession of phytoplankton biomass was investigated for a non-estuarine coastal lagoon situated in the northeastern Red Sea. Observations reveal that seasonal phytoplankton blooms inside the lagoon occur during a distinctively different period compared to the adjacent open sea. We provide evidence that this striking difference is due to the contrasting hydrodynamic conditions between inside and outside the lagoon, through their effects on stratification that regulate nutrient availability and hence favorable conditions to sustain rapid phytoplankton growth. The proposed mechanism may offer new insights into understanding the biophysical dynamics of non-estuarine coastal lagoons in other tropical regions of the global oceans.