Primary production in coastal bays and estuaries is influenced by physical factors such as wind, tides, freshwater inputs and light. In the short term, these elements affect phytoplankton biomass and nutrient availability. In Fangar Bay, a shallow, microtidal environment in the northwestern Mediterranean, spatial and temporal variations in phytoplankton concentration have been observed, closely linked to wind patterns. Regular sea breezes and strong northwesterly gusts generate stratification or mixing of the water column, influencing phytoplankton distribution. To analyse these processes, the ROMS model coupled to a NPZD (nutrient, phytoplankton, zooplankton, and detritus) scheme was used, with simulations compared to in situ measurements. Both observational and model results show that, with sea breezes (6 m·s-¹), phytoplankton concentrate at the surface due to stratification, whereas, with northwesterly winds above 10 m·s-¹, mixing of the water column homogenises nutrients and favours biomass increase in deeper layers. In addition, freshwater plumes from drainage canals affect the spatial distribution of phytoplankton. Numerical simulations confirm the relationship between these dynamics and satellite observations, showing the correspondence between model and real data. These findings provide key information to improve ecosystem management by optimising the interaction between freshwater inputs and prevailing winds. Strategies based on natural processes could help regulate phytoplankton growth and prevent eutrophication, promoting the sustainability of the bay.