The Guadiana estuary is a coastal system located in the southwest of the Iberian Peninsula and is the natural border between Portugal and Spain. It is a rock-bounded estuary which extends along more than 40 km and is characterized by a semidiurnal mesotidal regime. This paper represents an approach to the bedload transport across two flow sections located in the fluvial and marine domains. In the fluvial profile, the most frequent bedform is the plane bed. In the marine area the bed of the deep channel is composed of well-sorted sand, while a lateral bar displays partially cohesive sediments with dominant fine sands in a matrix of clayey silts. Data were acquired during spring and neap tides. Near-bottom water velocities were registered by an acoustic Doppler current profiler (ADCP). Density and bed rugosity were determined in sediment samples. These data were employed using Bagnold's equation (1963) to quantify the potential bedload (Qb). Further, real bedload values (Sb) were obtained by using Poliakoff traps. The comparison of the results of Qb under both ebb and flood conditions demonstrated a clear river-to-sea net transport in both sectors. The values of Sb were lower than those of Qb in every condition. The sand input across the fluvial estuary cannot supply the potential bedload in the lower domain of the channel, thereby causing a deficit that explains this lack of agreement between potential and real transport.