<p>The Indonesian Seas, a critical conduit between the Pacific and Indian Oceans, host dynamic nutrient exchanges that sustain high marine productivity. However, the mechanisms governing nutrient transport remain poorly quantified. Using an eddy-resolving coupled physical-biogeochemical model, this study diagnoses cross-basin nutrient fluxes and their drivers. The results indicate that in the water column above the annual mean maximum mixed layer depth (<i>Z</i>_MLDmax), the Makassar and Halmahera Straits serve as the primary nutrient inflow pathways, whereas the Timor Passage dominates nutrient export. Horizontal advection results in a net nitrate loss of −0.42×10¹²±0.41×10¹² mmol m⁻² d⁻¹, primarily driven by mean circulation, while eddy-induced transport contributes to nutrient replenishment. Vertical processes, particularly vertical diffusion, emerge as the dominant source of nutrients, supplying 1.57×10¹²±0.28×10¹²mmol m⁻² d⁻¹, accounting for 65% of the total input flux. Our findings imply the critical role of internal tides and eddy-driven mixing in sustaining surface productivity and regulating nutrient export. This study provides new insights into nutrient dynamics in the Indonesian seas and their implications for regional and global biogeochemical cycles.</p>