Coastal lagoons are shallow water bodies connected through narrow inlets, and their varying hydrographic conditions lead to distinct ecological characteristics providing important ecosystem services. Sharma is a restricted coastal lagoon ( \(\sim\) 150 km2) surrounded by pristine coral reefs in the northern Red Sea (NRS), and it holds significant value as it is part of Saudi Arabia’s NEOM ongoing gigaproject. Previous research revealed a remarkable anomalous phytoplankton seasonality within the lagoon compared to the rest of the NRS waters, with the lagoon exhibiting a late summer peak, opposite to the winter/spring peak in open waters. Here we aim to identify the physical mechanisms driving this phytoplankton phenology paradox and support informed decision-making for the lagoon’s future. To investigate the driving mechanism of phytoplankton phenology inside the lagoon, we utilised regionally-tuned satellite chlorophyll-a data (Sentinel-3 OLCI), in situ cruise measurements, and outputs from a high-resolution numerical model (Delft3D). We reveal several hydrodynamic differences between winter and summer that collectively alter stratification strength and nutrient availability within the lagoon due to its enclosed nature. Tidal oscillations modulate lagoon exchange, with seasonal density differences altering stratification and mixing. In summer, this density difference diminishes, and flood tides can induce mixing, especially during the day. Additionally, diurnal heat fluxes, particularly the summer nighttime heat loss from evaporation, enhance vertical mixing and ultimately nutrient availability. Following our findings, we provide recommendations to the NEOM project stakeholders targeting to sustain Sharma’s ecosystem services by maintaining this natural phytoplankton phenology paradox.
