In the last decades, so‐called internal or sea‐based mitigation measures have been suggested as nature‐based solutions to remove nutrients and improve water quality in semi‐enclosed coastal waters. However, these have rarely been tested in the field, especially in colder climates where winter ice cover is common. The aim of this experimental research was to investigate plant growth conditions in such an environment, as well to estimate nutrient removal capacity by harvesting constructed floating wetlands (CFWs). We tested small (24–28 m2) CFWs (Biomatrix®, Scotland, UK) at two demonstration sites: the Curonian lagoon (CL, Lithuania) and Szczecin lagoon (SL, Poland). In the CL, CFWs were planted predominantly with Carex acutiformes (Ehrh.), while the SL CFW was planted mainly with the reed Phragmites australis (Cav.) Trin. ex Steud. We aimed to test the amount of nutrient removal by plant harvesting over three subsequent years (2019–2021). We investigated carbon storage capacity and plant nutrient stoichiometry as indicators of potential nutrient limitation in the brackish coastal waters. Plant biomass increased annually, stabilising at 2.5–3.7 kg wet weight m−2. The total nutrient uptake per installed island area varied with the plant species composition. In the successive years, the harvested plants from the CL CFW dominated by Carex accumulated 10.4–13.1 g N m−2, 0.6–0.8 g P m−2 and 318–431 g C m−2 per year. The harvest from the SL CFW dominated by Phragmites contained a two‐times higher amount of nutrients, the respective figures being 21.2 g N m−2, 1.6 g P m−2 and 704 g C m−2. The nutrient stoichiometry in the vegetation did not suggest the presence of sub‐optimal growth conditions due to nitrogen limitation. However, the CL's dissolved nutrient supply was very low during the summer cyanobacteria bloom and indicated a severe nitrogen deficiency (as reflected in the dissolved inorganic nitrogen:dissolved inorganic phosphorus [DIN:DIP] molar ratio of 6). We suggest that to maximise nutrient removal capacity, tall plants with high biomass should be selected and/or plants with fine root systems to efficiently uptake the limiting nutrient from the water.