Estimates of bed roughness used for predictions of sediment transport are usually derived either from simple scalars of the physical roughness (i.e., ripple height or grain size) or from the hydrodynamic roughness length (Zo) based upon velocity gradient estimates in the benthic boundary layer. Neither parameter accounts for irregular bed features. This study re-evaluates the relation between hydrodynamic roughness and physical bed roughness using high-resolution seabed scanning in the inlet of a shallow lagoon. The statistically-robust relationship, based on a 1D statistical analysis of the seabed elevation at different locations of the Cabras lagoon. Sardinia, has been obtained between Zo and the topographical bed roughness Ks by defining Ks = 2*STD + skin friction, with STD the standard deviation of the seabed elevation variations. This correlation between Ks and Zo demonstrates that the roughness length is directly influenced by irregular bed features, and that the Reynolds number accounts for the total drag of the bed: the data points collapse on the Law of the Wall curves with a fitting factor x = 0.5. Further testing must be done in other locations and in the fully-rough domain in order to test how widely those new parameters can be applied.