## 2 Materials and Methods
### Microcosm Experiments  
_Phragmites australis_, sediment in contact with plant roots and sand used to assemble the CW systems, were collected in the Lima River estuary (north of Portugal). _P. australis_ were collected with the sediment attached to their belowground structures which were removed and brought to the lab to be used as plant root substrate. Plants with good physiological condition and similar biomass were selected. Six CWs were assembled at lab scale simulating a vertical flow configuration (VFCW), as described in [23], and adapted to operate with an automatically recirculating water system (flow rate ca. 10 mL\(\cdot\)min\({}^{-1}\)) as described in [24], with a recirculation period of 12 h followed by a 12 h non-recirculation period (Figure S1). Water level was maintained just above the substrate surface, i.e., the CWs substrates were kept at their water saturation level. Each microcosm was set up in plastic boxes (56 \(\times\) 39 \(\times\) 28 cm). Each box had three layers: the top layer was the plant roots' bed substrate, composed by sediment and sand mixed in a proportion of 1:2 (16 cm), the intermediate layer containing the porous substrate lava rock (2 cm) and the drainage layer on the bottom which was filled with gravel (4 cm). The top layer supported the _P. australis_ rhizomes and roots, maintaining the plant rhizosphere native microbial community. About 40 plants with stems of the same length and in good physiological condition were transplanted to each microcosm. For simulating CWs conditions, each box was wrapped in aluminum foil. After assembling, systems were acclimatized for one week with Hoagland nutrient solution to provide suitable nutritional conditions to plants. Then, the six CWs systems were irrigated with 1.5 L of water from the urban stream Ribeira de Joane for two weeks to complete the acclimization of the systems. The water from Ribeira de Joane used in the experiments was collected weekly from its mouth located next to Paraiso beach in Matosinhos, Portugal (41\({}^{\circ}\)13\({}^{\prime}\)33.5\" N, 8\({}^{\circ}\)43\({}^{\prime}\)00.4\" W). The Ribeira de Joane runs 3.7 km through a very urbanized area, being mainly canalized. This urban stream receives untreated wastewater as well as storm water, being a crucial element in the rural activity located along the stream banks. Two experiments were carried out to test two different groups of phenolic compounds. For each experiment, experiments were initiated after the acclimatization period mentioned above. Experiment#1 was carried out in spring of 2018, evaluating the removal of a mixture of NP and OP. Experiment#2 was carried out in spring of 2019, after re-assembling CW microcosms with new materials similarly to that described above, evaluating the removal of PCP. For each experiment, three of the microcosms (defined as CWs doped) were weekly irrigated with 1.5 L of Ribeira de Joane water doped with 100 \(\mu\)g\(\cdot\)L\({}^{-1}\) of each target compound (NP and OP in experiment#1 and PCP in experiment#2). The doping concentration was based on real concentrations previously found in environmental waters [25]. In each experiment, the other three microcosms (defined as CWs control) were irrigated only with 1.5 L of Ribeira de Joane water, each. Ribeira de Joane water, doped or not doped (control), was treated in one-week cycles over eight weeks per experiment. Therefore, after one week the CWs water was completely drained and new water (not-doped or doped) was added. Water losses by evapotranspiration processes were daily compensated by adding deionized water. For each experiment, the six CWs systems were kept under \"greenhouse\" conditions, namely in a nature light cycle.