Background, aim, and scope Bahía Blanca estuary is characterized by the occurrence of large intertidal areas, including both naked tidal flats and salt marshes densely vegetated with Spartina alterniflora. The estuary is strongly affected by human activities, including industrial and municipal discharges, harbor maintenance, cargo vessels and boat navigation, oil storage and processing, etc. Even numerous studies have reported the occurrence and distribution of heavy metals in sediments and biota from this estuary, although the function of the halophyte vegetation on metals distribution was at present not studied. The main objective of the present study was to understand the potential role of the salt marshes as a sink or source of metals to the estuary, considering both the obtained data on metal levels within sediments and plants from the studied areas at naked tidal as well as vegetated flats. Materials and methods The selected study area, named Villa del Mar, was located in the middle estuary coast. The sampling was carried out under low tide conditions, and the sampling area was divided into two parts: A (close to Villa del Mar) and B (north-westerly of Villa del Mar). In each part, two integrated samples of S. alterniflora (the first in the medium-salt marsh and the second in the higher one) were collected. Also sediments associated with the roots of S. alterniflora were taken at the same locations, in addition to another sediment sample from the naked zones of the tidal flats (without any vegetation). After corresponding treatment at the laboratory, plant and sediment samples were mineralized according to Marcovecchio and Ferrer, J Coast Res 21:826-834, 2005), in order to measure their metal concentrations by atomic absorption spectroscopy (AAS). Analytical quality (AQ) was checked against certified reference materials from NIES, Tsukuba (Japan). Results Most of the Spartina samples have shown highest Cd and Mn concentrations in the aerated parts of the plants, indicating an allocation process from the roots up to the leaves. Most of the samples have presented non-detectable Pb and Cr values. Cu, Fe, Ni, and Zn have presented highest concentrations in the underground parts of the plant, suggesting an accumulation process in the roots and rhizomes. In the case of sediments, samples from those sites