This article describes the transport processes and net salt flux within a shallow estuarine system, with particular reference to the Coombabah Lake–Creek system in Queensland, Australia. Observations of currents and salinity at two locations within Coombabah Lake provided a basis for assessing the relative importance of various transport processes within a very shallow (water depth <1 m) subtropical estuary. The instantaneous velocity and salinity data were decomposed into time-averaged means and time-varying components and were used to quantify the salt flux components attributed to various physical processes. In this study, advection by residual flow, which contributed 65% of the total salt flux, was identified as the dominant process in transporting salt. The advective flux also determined the direction of the net salt flux within this shallow estuarine system. This study concludes that the net salt flux varies spatially and temporarily with hydromorphological and meteorological conditions.