Emergent plant species growing in Andean natural wetlands have shown efficient phytoremediation capabilities in wetlands polluted by acid mine drainage. However, the types and amounts of heavy metals accumulated by native plant species are not well understood. In this study, we focused on determining heavy metal concentrations and bioaccumulation factors in Calamagrostis ligulata and Juncus imbricatus. Two acid wetlands located above 3,500 m a.s.l. in Ancash, Peru were assessed. Physico-chemical parameters and heavy metals concentrations in control and experimental plant samples were measured in dry and rainy seasons. Results indicated that C. ligulata and J. imbricatus aerial parts accumulated higher amounts of Fe, Zn, As and Al. Also, bioaccumulation factors revealed notable increases in As, Pb and Al, but less so in Cd, Fe and Zn. On the other hand, physico-chemical parameters of water quality (pH, temperature, dissolved oxygen, sulphides) between inflow and outflow of wetlands indicated significant differences in the presence of metals in comparison with their maximum permissible limits. Both emergent plant species showed an accumulation of heavy metals and thus the ability to recovery of water quality in wetland outflows. © 2012 Springer Science+Business Media B.V.