The bottom boundary layer (BBL) dynamics play an important role in regulating the energy, momentum balance, and circulation in the shallow shelf areas. Unlike previous studies that disconnected BBL with background variable shelf circulation, we investigate the dynamic connection between the wind-driven shelf circulation and BBL dynamics, and show the spatial characteristics of BBL dynamics in response to three-dimensional (3D) heterogeneous transport over the highly variable shelf topography in the Northern South China Sea. Our process-oriented modeling study demonstrates that the mixing dynamics and upslope buoyancy transport over varying shelf topography alter the spatial variability of BBL dynamics. Driven by southwesterly upwelling-favorable winds, the along-shelf current generated a frictional upslope Ekman transport. The along-isobath pressure gradient force (PGFx & lowast; $PG{F}<^>{{x}<^>{\ast }}$) formed by the flow-topography interactions over the meandering shelf induces the geostrophic cross-isobath transport. The downwave (upwave) PGFx & lowast; $PG{F}<^>{{x}<^>{\ast }}$ enhances (offset) the frictional upslope transport over the east (west) of the shelf that has a concaving (uniform) bottom topography. Over the eastern shelf with concave isobaths, the intensified PGFx & lowast; $PG{F}<^>{{x}<^>{\ast }}$ and upslope cross-isobath dense water transport strengthen stratification and weaken the effect of bottom stress-induced mixing, limiting the development of the BBL. The antithesis occurs over the western shelf, where a small bottom stress controls the BBL. River discharge and the tidal current modulate the alongshore current, upslope transport, bottom stress intensity, and BBL development. We model the trajectory of seabed particles as they respond to the BBL dynamic regimes, and find that high (low) concentration, short (long) suspension time, and strong (weak) shoreward transport occurover the eastern (western) shelf, respectively. This study investigated the dynamics impact of wind-driven upslope transport on the bottom boundary layer (BBL). The BBL is a thin, turbulent layer of water above the seafloor that plays an important role in regulating the transport of sediment and other substances, as well as the energy and momentum balance in shallow shelf waters. We used a process-orientated numerical model to investigate how wind-driven currents interact with the shelf topography and what is the impact of the interaction on forming different BBL regimes in the northern South China Sea. We found that the current-induced instability (determined by current intensity) and the upslope buoyancy transport-induced stabilizing process (determined by current direction) jointly balance the BBL dynamics. Topographic characteristics over the southwestern and southeastern shelves off the Pearl River Estuary (PRE) regulated the intensities and directions of the bottom layer currents, controlled dynamics balance in the BBL and thus formed different BBL regimes. The BBL was further modulated by the river plume from the PRE and tidal currents over the shelf. The BBL dynamics is highly variable due to topographically regulated wind-driven circulation and transport over the continental shelf. The competition between flow-induced shear mixing and upslope buoyancy transport governs the bottom boundary layer dynamics over a variable shelf The mixing and buoyancy transport are highly regulated by variable flow-topography interaction and modulated by plume and tidal forcing A varying bottom boundary layer shapes the characteristics of particle transport
