Estuaries and coastal bays are areas of large spatio-temporal variability in physical and biological variables due to environmental factors such as local wind, light availability, freshwater inputs or tides. This study focuses on the effect of strong wind events and freshwater peaks on short-term chlorophyll a (Chl a) concentration distribution in the small-scale and microtidal, Fangar Bay (Ebro Delta, northwestern Mediterranean). The hydrodynamics of this bay are primarily driven by local wind episodes modulated by stratification in the water column. Results based on field-campaign observations and Sentinel-2 images revealed that intense wind episodes from both NW (offshore) and NE-E (onshore) caused an increase in the concentration of surface Chl a. The mechanisms responsible were horizontal mixing and the bottom resuspension (also linked to the breakage of the stratification) that presumably resuspended Chl a containing biomass (i.e., micropyhtobentos) and/or incorporated nutrients into the water column. On the other hand, sea-breeze was not capable of breaking up the stratification, so the chlorophyll a concentration did not change significantly during these episodes. It was concluded that the mixing produced by the strong winds favoured an accumulation of Chl a concentration, while the stratification that causes a positive estuarine circulation reduced this accumulation. However, the spatial-temporal variability of the Chl a concentration in small-scale estuaries and coastal bays is quite complex due to the many factors involved and deserve further intensive field campaigns and additional numerical modelling efforts.