The complex circulation for both atmospheric and ocean affects the pathways of floating marine debris (MD). The aim of this research was to define the MD trajectories in the Indonesian boundary seas. The Lagrangian particle method was applied with oceanographic factors and debris classes based on 1 to 3% windage class. The simulation was applied during the Northwest and Southeast Monsoon period. On the basis of the obtained findings, the debris trajectory patterns were indicated to vary in the two monsoons. In the northern part of Indonesia, all neighbouring countries were affected, especially those near the boundaries. In the southern part of Indonesia, most of the debris headed west towards the Indian Ocean. MD was mostly transported by the ocean currents and monsoonal wind and ended up in the coastal area. Some debris was also still floating in the open ocean after three months. This study concluded that marine litter not only polluted Indonesia water, but also the neighbouring countries.