A three-dimensional process-oriented model is applied to explore the circulation in the Arafura Sea during the southeasterly monsoon. During this period, widespread phytoplankton blooms develop in a large area (300 km × 300 km) in the northwestern Arafura Sea. The model findings indicate that undercurrents are the principal source of nutrient-rich Banda Sea slope water for the region. It is demonstrated that these undercurrents operate to flush the northwestern Arafura Sea with Banda Sea slope water on a time scale of 1-3 months, which is consistent with observational evidence. The simulated undercurrents are the signature of the classical lee effect, frequently observed in lakes, that comes into play in the Arafura Sea given its bay-like geometry, shallow-water depth (40-50 m), and close vicinity to the equator. It is also shown that density stratification and rotational effects have important influences on the pathway and intensity of the overturning circulation in the northwestern Arafura Sea, which needs to be further explored in the future.