Abstract Wetland macrophytes play many important indirect roles in constructed wetlands with horizontal subsurface flow (HF CWs) including insulation of the bed surface during winter, provision of substrate for attached bacteria in the rhizosphere or oxygen leakage into anoxic rhizosphere. In the Czech Republic, HF CWs are mostly planted with Phragmites australis (Common reed) or Phalaris arundinacea (Reed canarygrass) or with a combination of these two species. The early systems were planted only with Phragmites according to the then available information from abroad. Later, Phalaris was used because of easy planting and fast growth. In 2011, macrophyte survey of 55 HF CWs in the Czech Republic was carried out with the aim to identify “weedy” species, i.e., species which were not originally planted. During the survey, 83 macrophyte “weedy” species were recorded with more species being found in the outflow zone (74) as compared to inflow zone (46). However, most species were found only as individual plants in the filtration bed margins with the exception of Urtica dioica (Stinging nettle) in the inflow zone and Epilobium hirsutum (Hairy willowherb) in the outflow zone of several systems. It has been found that the number of “weedy” species decreases with increasing length of operation. In systems, where “weedy” species overgrew the originally planted species, treatment efficiency was not affected.