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The Banda Sea is of crucial importance for the circulation of the world's oceans, as it is part of the connection between the Pacific to the Indian Ocean. One peculiarity of the upper ocean hydrography in the Banda Sea is the occurrence of barrier layers. The regionality and temporal variability of barrier layer thickness (BLT) in the Banda Sea are examined in this study utilizing in‐situ observations and ocean reanalysis output. It is found that a barrier layer occurs in over 90 % of the observational data profiles, and in over 72 % of those profiles, the BLT is shallower than 10 m. Furthermore, we find a seasonal cycle in BLT with a maximum thickness of about 60 m occurring during austral autumn and winter and coinciding with the presence of low saline waters fed by the regional river discharge and rainfall from the Java Sea and Makassar Strait. In addition, we identify the existence of a quasi‐permanent anticyclonic circulation cell in the Banda Sea that may support the trapping of surface freshwater by retention. The anticyclonic circulation is most likely wind‐driven because it coincides with the regional Ekman pumping pattern. Modulation of the anticyclone is via seasonal variability in the wind stress curl which in turn may explain the efficiency of freshwater retention and thus the BLT. The annual mean BLT distribution in the Banda Sea shows a preferential region of thickened barrier layers around 6o‐8oS and 124o‐126oE and resampling the pattern of the monthly mean climatology. Plain Language Summary: The Banda Sea is crucial to the circulation of the world's oceans and atmosphere due to its location within the equatorial regions of the Indonesian Maritime Continent. It links the Pacific and Indian Oceans' circulation via the Indonesian Throughflow and contributes to driving atmospheric conditions via heat and moisture fluxes. Strong salinity‐stratified barrier layers insulate the water exchange between the surface and subsurface. The formation and seasonal variation of barrier layer thickness (BLT) in the Banda Sea are analyzed based on all available observations and ocean reanalysis outputs. Observations show that the Banda Sea has a barrier layer for the most part of the season. The BLT maximum appears during austral winter (June to August) months. The seasonal BLT maximum is attributed to the near‐surface water freshening, which shoals the mixed layer depth (MLD) and deep isothermal layer depth (ILD) maintained by a steady anticyclonic gyre. Other processes, such as wind stress curl‐induced Ekman pumping associated convergence, also modulate its seasonal variability. Key Points: First study estimating barrier layer thickness (BLT) in the Banda Sea using comprehensive observationsA quasi‐permanent barrier layer exists in the Banda Sea with seasonal variation in occurrence and thicknessThe intrusion of low saline waters and anticyclonic circulation are identified as the main mechanisms for creating and modulating the local BLT [ABSTRACT FROM AUTHOR]