Sediment cores and flooding water were collected at 0, 5, 10 and 50 min of tidal inundation in two sites of the Rosário salt marsh located in the proximity of a heavy industrialised zone of Tagus estuary colonised by pure stands of Spartina maritima (low marsh) and Sarcocornia fruticosa (high marsh). The cores were sliced in 5 cm layers and sediment solids, pore water, and belowground biomass were separated in order to measure Fe, Mn, Zn, Cu, Pb and Cd. The pore waters and sediments colonised by S. fruticosa, as well as belowground biomass presented high concentrations of Zn, Cu, Pb and Cd. Belowground biomass exceeded in one order of magnitude the metal levels in sediments. Abundant belowground biomass and small dimension of S. fruticosa roots facilitates the root-sediment interactions and presumably the metal retention in the higher marsh. The novelty of this work is the result of tidal inundation on pore water concentrations of metals in salt marsh sediments and their exportation to the water column. Concentrations in pore waters varied at minute scales, but 50 min after inundation levels were comparable to the initial values. The metal levels in flooding water increased abruptly during the first 10-20 min of inundation. The concentration peaks (Fe = 60 μM, Mn = 7.5 μM, Zn = 1.7 μM, Cu = 550 nM, Pb = 100 nM, Cd = 1.7 nM) reached one to two orders of magnitude above the values found in subsequent periods of inundation. The advective transports during the 50 min inundation during two daily pulses of inundation were: Fe (9520 and 1640), Mn (24), Zn (220 and 82), Cu (74 and 16), Pb (13 and 15) and Cd (0.3 and 0.08) for S. maritima and S. fruticosa, respectively. These quantities exceeded three to four orders of magnitude of the corresponding predicted diffusive fluxes (Fick 1st law) on a daily basis. This work emphasizes the importance of tidal flooding over salt marsh sediments to the metal exportation to the water column.