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A constructed wetland system composed of a subsurface flow wetland, a surface flow wetland and a facultative pond was studied from July 2008 until May 2012. It was created to treat the domestic sewage produced by a hamlet of 150 inhabitants. Monthly physicochemical and microbiological analyses were carried out in order to evaluate the removal efficiency of each stage of the process and of the total treatment system. Pair-wise Student's t-tests showed that the mean removal of each considered parameter was significantly different (α = 0.05) between the various treatment phases. Two-way ANOVA and Tukey's HSD tests were used to find significant differences between wetland types and seasons in the removal efficiency of the considered water quality parameters. Significant differences in percent removal efficiency between the treatment phases were observed for total phosphorus, total nitrogen, ammonia nitrogen and organic load (expressed as Chemical Oxygen Demand). In general, the wastewater treatment was carried by the sub-superficial flow phase mainly, both in growing season and in quiescence season. Escherichia coli removal ranged from 98% in quiescence season to >99% in growing season (approximately 2–3 orders of magnitude). The inactivation of fecal bacteria was not influenced by the season, but only by the treatment phase.