The Berau Continental Shelf is located close to the Equator in the Indonesian Archipelago, hosting a complex of coral reefs along its oceanic edge. The Berau coral reefs have a very high biodiversity, but the area is under serious risk due to river-derived nutrients and sediments. The region is characterized by weak winds, moderate tides, and almost absent Coriolis forcing. Existing knowledge about river plume behavior in tropical environments is limited. The aim of this paper is to investigate the influence of the subtle physical forcing on the dynamics of the Berau river plume. A three-dimensional model (ECOMSED) was calibrated with observational data. The model was forced by freshwater input from the Berau river distributaries, tides at the open boundaries, and measured hourly wind. The model reproduces the freshwater dynamics on the shelf adequately and highlights that the river plume spreads symmetrically for river forcing only. Tides cause vertical mixing and suppress the cross-shelf spreading of the river plume. However, the spreading of the river plume over the shelf is mainly controlled by the weak monsoonal winds, resulting in a seasonal development. During the Southeast Monsoon, the southerly winds push the plume northeastward and cause a stratified water column in the northern part of the continental shelf. Northerly winds during the Northwest Monsoon disperse the plume to the south, promoting a vertically well-mixed water column. The results can be used to predict the possible impact of land-use changes in the steadily developing Berau region on coral reef health.