This work investigates the effect of plant species (Eucalyptus camaldulensis vs. Arundo donax) on carbon (C) turnover during wastewater application to the land. The study was carried out in 40-liter pots under field conditions and plant species were treated either with pre-treated municipal wastewater or freshwater. Plant species had a strong effect on soil organic matter with pots planted with E. camaldulensis showing greater values than pots planted with A. donax. In accordance, greater respiration rates were measured in E. camaldulensis pots compared to those planted with A. donax. The respiration rate followed a decreasing trend with the progress of the season for both species. These findings suggest differences in soil microbial community composition and/or activity in the rhizosphere of plant species. Minor effects of plant species or effluent were observed in dissolved organic carbon, protein, and hexoses content. In conclusion, the results of the present study reveal an important role of plant species on C cycling in terrestrial environments with potential implications on the sequestration of C and release of nutrients and pollutants. OPEN ACCESSWater 2015, 7 289