Long-term investigations were carried out in two pilot-scale horizontal subsurface flow constructed wetlands (planted and unplanted) with an iron-rich soil matrix for treating sulphate-rich groundwater which was contaminated with low concentrations of chlorinated hydrocarbons. The temporal and spatial dynamics of pore-water sulphide, Fe(II) and phosphate concentrations in the wetland beds were characterized and the seasonal effects on sulphide production and nitrification inhibition were evaluated. The results demonstrated that the pore-water sulphide concentrations gradually increased from less than 0.2 mg/L in 2005 to annual average concentrations of 15 mg/L in 2010, while the pore-water Fe(II) concentrations decreased from 35.4 mg/L to 0.3 mg/L. From 2005 to 2010, the phosphate removal efficiency declined from 91% to 10% under a relatively constant inflow concentration of 5 mg/L. The pronounced effect of plants was accompanied by a higher sulphate reduction and ammonium oxidation in the planted bed, as compared to the unplanted control. A high tolerance of plants towards sulphide toxicity was observed, which might be due to the detoxification of sulphide by oxygen released by the roots. However, during the period of 2009-2010, the nitrification was negatively impacted by the sulphide production as the reduction in the removal of ammonium from 75% to 42% (with inflow concentration of 55 mg/L) correlated with the increasing mean annual sulphide concentrations. The effect of the detoxification of sulphide and the immobilization of phosphate by the application of the iron-rich soil matrix in the initial years was proven; however, the life-span of this effect should not only be taken into consideration in further design but also in scientific studies.