An integrated pilot-scale treatment system consisting of a vertical subsurface flow (317 m2), a horizontal subsurface flow (229 m2) and a free water surface (240 m2) constructed wetlands operating in series for the treatment of a combined sewer effluent was put into operation and monitored over a period of about 1.5 years. The goal of the treatment system was to provide effluents suitable for various water reuse applications. Moreover, the influence of pulses of high flow resulting from several rain events over the treatment performance of the system was evaluated. An intensive sampling campaign was also carried out following an intense storm (45 mm in one-hour span) to have a further insight into the characteristics of the inflowing water at the early part of it or so-called ‘first-flush’. Results under dry weather conditions showed a good performance on the removal of BOD5, COD and TSS taking place already in the vertical flow wetland (94, 85 and 90%, respectively). A high removal of total nitrogen occurred also in the vertical flow wetland (66%) suggesting both nitrification and denitrification to take place, presumably due to the existence of both aerobic and anoxic microenvironments within the bed. Removal of Escherichia coli along the treatment system was of almost 5 log units. To this respect, the horizontal flow and free water surface wetlands proved to be crucial treatment units to achieve a water quality suitable for further reuse (e.g. recharge of aquifers by percolation through the ground, silviculture and irrigation of green areas non accessible to the public). Although the occurrence of the storm event caused a prompt raise of COD and TSS within the first 30 min of rainfall (868 and 764 mg L−1, respectively), it was soon followed by a dilution effect. In general the storm events did not jeopardize the correct functioning of the system, proving its robustness for the treatment of a combined sewer effluent.