© 2017 Taylor & Francis Group, LLC. Mexico's mercury mining industry is important for economic development, but has unfortunately contaminated soils due to open-air disposal. This case was seen at two sites in the municipality of Pinal de Amoles, State of Queretaro, Mexico. This paper presents an evaluation of mercury dynamics and biogeochemistry in two soils (mining waste soil) using ex-situ wetlands over 36 weeks. In soils sampled in two former mines of Pinal de Amoles, initial mercury concentrations were 424 ± 29 and 433 ± 12 mg kg−1 in La Lorena and San Jose, former mines, respectively. Typha latifolia and Phragmites australis were used and 20 reactors were constructed (with and without plants). The reactors were weekly amended with a nutrient solution (NPK), for each plant, at a pH of 5.0. For remediation using soils from San Jose 70–78% of mercury was removed in T. latifolia reactors and 76–82% in P. australis reactors, and for remediation of soils from La Lorena, mercury content was reduced by 55–71% using T. latifolia and 58–66% in P. australis reactors. Mercury emissions into the atmosphere were estimated to be 2–4 mg m−2 h−1 for both soils.