Two different Cymodocea nodosa (Ucria) Ascherson beds growing in mining-contaminated sediments were compared with two reference beds in the Mar Menor coastal lagoon. The accumulation of Zn, Pb and Cd in different fractions of the plant, the sediment parameters that regulate the availability of metals, the seabed structure and dynamics of each seagrass bed and its associated macroinvertebrate community were studied. C. nodosa accumulates metals from the sediments and reflects their bioavailability for this seagrass. At each station, the metal content of the rhizomes was lower than that of leaves and roots. The concentration of acid-volatile sulfides does not seem to influence the availability of metals to the seagrass, possibly due to oxygen transport to underground tissues. The highest metal concentration in all the contaminated stations was found in the leaf-biofilm, due to the formation of complexes between metals and the extracellular polymeric substances that form the biofilm. All the seagrass beds were seen to be undergoing expansion, those growing in contaminated sediments accumulating great quantities of metals and showing highest photosynthetic leaf surface area and highest leaf biomass. However, these structural parameters were not seen to be responsible for the differences in the faunal composition observed between contaminated and reference beds. Moreover, the multivariate analysis identified the metal content of leaves, biofilm and sediments as important variables that may be responsible for these differences in faunal composition. In this study we have demonstrated that both the seagrass C. nodosa and the biofilm on the plant leaves may be used as environmental tools in the Mar Menor lagoon. The former is an useful indicator of sediment contamination, whereas the latter seems to be a good sentinel of water quality.