Tropical mountain river systems that drain rainforests and experience tropical monsoons typically demonstrate high runoff and discharge a disproportionate amount of particulate load to the world’'s oceans compared with other more temperate river systems. As a typical tropical small mountainous river with an broad continental shelf system and wave dominated environment, the Kelantan River is one of the few north-flowing streams in Southeast Asia that discharges into the broad and shallow continental shelf of South China Sea. The existence of seasonal variations of salinity, turbidity, and sediment composition indicate that coarse-grained sediments are deposited rapidly when terrestrial sediments delivered by the Kelantan River leave the river mouth. They are then reworked by wave action during the rainy season, leading to the development and rapid migration of barrier spits near the west side of the river mouth. Under the influence of the seasonal variations in the river plume, fine-grained sediments discharged into the sea by the Kelantan River are transported both along-shore and cross-shore, and most of them are deposited in the continental shelf area within 10 km of the river mouth, because of rapid removal of sediments from the river plume. The spatial distribution patterns of sediment composition, C/N ratio, terrestrial organic carbon content, and Sr/Al ratio also support our conclusion. •Terrestrial materials are mainly buried near the estuary in small tropical mountainous river-shallow broad shelf system.•Wave action determines the coarse sediment transport that result in development and migration of sand spits.•River plume is the main controlling factor in fine-grain particle cross-shore and along-shore transport.