The Maluku Channel is a major opening of the eastern Indonesian Seas to the western Pacific Ocean, the upper-ocean currents of which have rarely been observed historically. During December 2012–November 2016, long time series of the upper Maluku Channel transport are measured successfully for the first time using subsurface oceanic moorings. The measurements show significant intraseasonal-to-interannual variability of over 14 Sv (1 Sv ≡ 10⁶ m³ s⁻¹) in the upper 300 m or so, with a mean transport of 1.04–1.31 Sv northward and a significant southward interannual change of over 3.5 Sv in the spring of 2014. Coincident with the interannual transport change is the Mindanao Current, choked at the entrance of the Indonesian Seas, which is significantly different from its climatological retroflection in fall–winter. A high-resolution numerical simulation suggests that the variations of the Maluku Channel currents are associated with the shifting of the Mindanao Current retroflection. It is suggested that the shifting of the Mindanao Current outside the Sulawesi Sea in the spring of 2014 elevates the sea level at the entrance of the Indonesian Seas, which drives the anomalous transport through the Maluku Channel. The results suggest the importance of the western boundary current nonlinearity in driving the transport variability of the Indonesian Throughflow.

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 6^o‐8^oS and 124^o‐126^oE and resampling the pattern of the monthly mean climatology.