Abstract The Seram and Banda Seas (SBS) convey the eastern pathway of Indonesian Throughflow (ITF) from Maluku and Halmahera inflow portals. This study aims to investigate circulation and variability at near-surface and thermocline layers in the SBS region using validated INDESO model output datasets (2008-2015). It is shown that much warmer and saltier thermocline ITF water (24,36°C and 34,65 psu) from Halmahera is predominant, flowing southward and impinging on the northern coast of Seram near 128.5°E. The flows then bifurcate eastward into the Banda outer ring arc and westward into Banda via the Manipa Strait and western Seram Seas. In Banda, two clockwise eddies are found related to these inflows. Secondary southward inflow via Lifamatola is associated with cooler and less salty water (23,3°C and 34,45 psu), which merges with ITF Halmahera. The variability of oceanographic parameters is dominated by the annual period. However, on an interannual scale, the response of seawater temperature to ENSO is evident, and its amplitude, as shown by the principal component time series EOF, is much stronger in Banda than in Seram at -2.7. A decreasing trend of seawater temperature was also found in 2015.