This paper derives local formulae to estimate bed roughness and suspended transport and present a method to calculate net sediment transport at tidal inlet systems, combining field data and a range of well established empirical formulations. To accomplish this, measurements spanning a spring-tidal cycle of mean water levels, waves, near-bed flow turbulence and bed forms were obtained from the Ancão Inlet, Ria Formosa lagoon system, Portugal. High-resolution hydrodynamic data were gathered using acoustic equipments and by measuring sediment properties (grain-size diameter and bed form dimensions) under fair-weather conditions. The results compared favourably with available direct and indirect field observations of sediment transport rates. The approach appears to be robust and widely applicable and so can be applied to the same conditions in any tidal inlet system. This is of particular importance when attempting to understand sediment transport at inlet mouths, and has practical applications in a range of coastal engineering and coastal management areas concerned with navigation safety, coastal erosion, ecosystem health and water quality. The study discusses the applicability of the method on evaluating system flushing capacity, giving important insights on multiple inlet evolution, particularly with regard to their persistence through time. The methodological framework can be applied to assess the long-term stability of single- and multiple-inlet systems, provided that estimates of sediment storage at ebb-tidal deltas are available and sediment transport estimates during storm events are statistically considered.