Sediment dynamics have great effects on the morphology of estuaries and deltas. As riverine sediment input has decreased in many estuaries in recent years, the removal and dispersion of sediments by currents and waves inside estuaries has assumed a more dominant role; however, the overall effects of waves are less well understood. In this study, we used the Coupled Ocean Atmosphere Wave Sediment Transport system to model the effects of waves on sediment transport in China's Pearl River Estuary. The results indicate that the presence of waves increased the landward current and sediment transport at the bottom of the channel and the seaward fluxes of water and sediment at the West Shoal, which is the main shallow area that accepts riverine sediment. Relative to the case without waves, the effects of waves increased the estuary's total sediment export by 45% to 9.14 megatons in one typical year, which even exceeded the annual riverine load in the year. The dry winter season shows the highest wave effects on sediment budget, and the sediment export was increased by 86% to 2.59 megatons with waves when compared with that without waves. This increase export was mainly concentrated at the surface near the western shore. Moreover, the waves increased lateral sediment entrapment in the Southwest Shoal, which explains the local geomorphologic evolution in recent decades. This study is of implication for the study on sediment exchange between shoal and channel in estuaries and on the fates of riverine sediment from source to sink.