This work describes the physical oceanography at successively smaller scales, from that of the eastern Indian Ocean, to the shelf from NW Cape to Cape Leeuwin, down to the Marmion lagoon. At the largest scale, the primary tool is the global Ocean Forecasting Australia Model (OFAM), that has coarse (>2 degree) resolution distant from Australia, but has 0.1 degree (~10 km) resolution in the Australasian region. Being global, OFAM simulates the longshore pressure gradient, largely due to the Indonesian Throughflow, that drives the Leeuwin Current southward along the shelf break of the WA coast. The model provides good qualitative representation of the Leeuwin Current and its associated eddies but, at 10 km resolution, tends to underestimate the current speeds on the shelf and cross-shore fluxes. OFAM output has been corrected with observations (in a separate CSIRO project) and archived to provide nearly 2 decades of ocean conditions. As a prelude to later biological investigations, it is used to investigate the longshore connectivity of shelf waters, demonstrating that the shelf can be classified into several sections of alternating low and high retention. At this scale, openocean swells are important, with biological particles near the surface being driven north-east under their influence. At the next level, the Rutgers Ocean Modelling System (ROMS) is nested inside OFAM, covering the southern west shelf, with resolution down to 2 km near the coast. ROMS produces similar patterns of circulation to OFAM, but the Leeuwin Current and inshore wind-driven currents are narrower and stronger. The ROMS model is used primarily to drive a model of primary productivity over the shelf. ROMS produces eddies that correspond well with those observed in sea-surface temperature images, and also shows instances of intermittent upwelling along the shelf break. Upwelling and eddy transport prove to be significant mechanisms for moving nutrients and phytoplankton on and off the shelf, respectively. At the scale of the Marmion lagoon, surface waves breaking on the reefs drive currents in the lagoon. The present study incorporated a year-long measurement program to quantify the reef and lagoon circulation. At low wave heights, the lagoonal circulation is driven primarily by longshore winds. However, when the incoming waves are higher than about 1.5 m, they break on the reef, carrying water into the lagoon, and causing currents to the north and south out of the lagoon. Modelling of reef dynamics requires very high resolution, down to tens of metres, and a model that includes both waves and currents. Two model configurations have been used in the present study: ROMS together with the wave model SWAN, and Xbeach, a littoral-zone model still under development at Delft University. Xbeach accurately represents the lagoonal dynamics.