Results are presented for new laboratory-scale numerical simulations of bi-directional stratified flows generated within an idealized trapezoidal sill-channel topography, focussing on the lateral (or secondary) flow structure across the channel both in non-rotating and rotating frames of reference. The simulations utilise the non-hydrostatic Bergen Ocean Model (BOM), a three-dimensional general ocean circulation model. The results from the BOM simulations are verified by large-scale experimental data obtained in the LEGI Coriolis rotating platform in Grenoble, within which velocity and density fields for bi-directional stratified flows were measured through particle image velocimetry (PIV) and micro-conductivity density probes, respectively. The BOM simulations reproduce the main dynamic flow patterns and structure of the large-scale exchange flows generated through the trapezoidal sill-channel, with the lower layer saline intrusion flux shown to reduce, due to partial blockage, as the upper freshwater flow is increased (i.e. net barotropic forcing). Non-rotational BOM simulations show upward (and downward) flow along the centreline of the trapezoidal sill-channel in the upper (and lower) layers, with symmetrical counter-rotating circulation cells forming both above and below the density interface. By contrast, equivalent BOM simulations within a rotating frame of reference show the secondary flow circulation in the lower dense water layer to be dominated by Ekman dynamics, while two co-rotating cells are formed in the upper freshwater layer above the inclined density interface. In these rotational cases, significant upward and downward velocities (i.e. strong upwelling and downwelling) are generated adjacent to the inclined sill-channel side walls (in comparison to non-rotating cases). This secondary flow effect may be especially relevant for exchange flows in estuaries, fjords, deep-ocean channels and sea straits, where the channel width exceeds the Rossby radius of deformation and, thus, Earth rotation effects become important dynamically. In particular, any potential vertical transport pathway associated with this upwelling and downwelling at the inclined channel side slopes may have strong managerial implications in coastal areas, whereby tracers (e.g. contaminants, salinity, reduced DO waters, fine sediments) can be transferred from deep waters to the near surface.