In order to evaluate the Stuckenia filiformis plant species as an indicator organism of heavy metal pollution in biomonitoring studies of the aquatic ecosystem, the aim of this study was to determine the levels of heavy metal accumulation (Co, Cu, Fe, Mn, Ni, Pb and Zn) in leaves of the submerged macrophyte S. filiformis and the possible relationship of the concentrations of these metals with those found in surface water and sediment samples of the Suquía river. Sampling was carried out in July 2006 and February 2009, during the dry and wet seasons, respectively, at 7 sampling sites where three replicates of surface water, sediment and S. filiformis plants were collected. Cobalt, Ni and Zn in surface water were significantly higher in the samples collected in 2006 than those in 2009. In sediment, the concentrations of Co, Cu, Ni, Pb and Zn, along with organic matter, were significantly higher in 2006, while those of Fe were significantly greater in 2009. Copper and Pb exceeded the limits established for the protection of aquatic life by national (Cu: 2.0µgL−1, Pb: 2.0µgL−1) and international organizations (Cu: 1.6µgL−1, Pb: 2.5µgL−1) in surface water, while in sediment, Zn exceeded the limit for ecological screening levels (Zn: 121.0mgkg−1) in 2006. In the surface water and sediment samples, heavy metal concentrations were found to be higher downstream of Córdoba city (Sites 6 and 7) in both sampling campaigns, probably related to the contribution of pollutants from the effluent discharge of a wastewater treatment plant and industrial activities of the city. The aquatic plant S. filiformis showed a high capacity to accumulate heavy metals in its tissues, in areas of the river where higher values of heavy metals in the abiotic compartments surface water and sediments were observed. Copper, Pb and Zn incorporated as contaminants in surface water and sediments were able to be removed by S. filiformis by self-purification processes. Therefore, this species could be proposed as a suitable heavy metal bioindicator for the early stages of pollution in rivers.