Western boundary currents strongly influence the dynamics on the adjacent continental shelf and in particular the cross-shelf transport and uplift through the bottom boundary layer. Four years of moored in situ observations on the narrow southeastern Australian shelf (in water depths of between 65 and 140 m) were used to investigate bottom cross-shelf transport, both upstream (30 degrees S) and downstream (34 degrees S) of the separation zone of the East Australian Current (EAC). Bottom transport was estimated and assessed against Ekman theory, showing consistent results for a number of different formulations of the boundary layer thickness. Net bottom cross-shelf transport was onshore at all locations. Ekman theory indicates that up to 64% of the transport variability is driven by the along-shelf bottom stress. Onshore transport in the bottom boundary layer was more intense and frequent upstream than downstream, occurring 64% of the time at 30 degrees S. Wind-driven surface Ekman transport estimates did not balance the bottom cross-shelf flow. At both locations, strong variability was found in bottom water transport at periods of approximately 90-100 days. This corresponds with periodicity in EAC fluctuations and eddy shedding as evidenced from altimeter observations, highlighting the EAC as a driver of variability in the continental shelf waters. Ocean glider and HF radar observations were used to identify the bio-physical response to an EAC encroachment event, resulting in a strong onshore bottom flow, the uplift of cold slope water, and elevated coastal chlorophyll concentrations.