The impact of urbanization, industrialization, agriculture, mining, and stormwater runoff on ecosystems has resulted in significant water pollution concerns worldwide. Significant attention has been paid to the removal of potentially toxic elements (PTE) and metalloids (e.g., arsenic (As), selenium (Se) and lead (Pb)) by various plant species. However, little research has been published on the simultaneous accumulation of cadmium (Cd), chromium (Cr), and nutrient removal, by floating treatment wetlands (FTW), from stormwater runoff, and the accumulation and recovery of rare earth elements (REE) through energy biomass cultivation. This research bridges knowledge gaps in the remediation of REE using short-rotation willow (Salix spp.) and simulated stormwater remediation of Cd and Cr with Phragmites australis and Iris pseudacorus. In this context, three different microcosm experiments were conducted with perennial plants (P. australis and I. pseudacorus) in FTW. Stem growth, dry biomass, root length, chlorophyll content index (CCI), anatomical plant tissue changes, Cd accumulation and N and P removal from simulated stormwater were investigated over a 50-days period under different Cd doses (0, 1, 2 and 4 mg L−1). In addition, the effects of Cr dose (0, 500, 1000 and 2000 μg L−1) on the growth and anatomy of P. australis and I. pseudacorus, as well as on the accumulation of Cr in plant biomass and N and P removal were studied in FTW over a 50-day period. In addition, the effects of REE doses on stem growth, dry biomass, root length and their accumulation in biomass were investigated in two Salix species (S. myrsinifolia and S. schwerinii) and two cultivars (Klara and Karin) in FTW over a 28-day period. The REE treatments contained a single-dose of lanthanum (La: 50 mg L−1), multi-solute of six-REE (La: 11.50 mg L−1 + yttrium (Y: 11 mg L−1) + neodymium (Nd: 10.50 mg L−1) + dysprosium (Dy: 10) + cerium (Ce: 12 mg L−1) + terbium (Tb: 11.50 mg L−1)) and control (without REE). Moreover, REE recovery from biomass ash after combustion was investigated. In this study, P. australis and I. pseudacorus growth parameters were not hampered by Cd stress, their roots accumulated more Cd than the shoots and were capable of lowering N and P concentrations. The impact of Cr was more evident on plant growth under the low- and medium doses (500 and 1000 μg Cr L−1). However, anatomical changes were observed under the high dose (2000 μg Cr L−1, respectively). Both species were able to remove a substantial (98−99%) concentration of N and P within a 10-day period of increased Cr loading. The greatest amount of Cr was retained in P. australis and I. pseudacorus roots. Salix species and cultivars did not show REE toxicity symptoms and displayed a strong growth response compared to the control. All Salix accumulated REE in their biomass, although the greatest amounts of accumulated REE were found in the roots of the Klara and Karin cultivars. The substantial deposition of Cd and Cr in the roots of P. australis and I. pseudacorus, and REE in the Salix roots show their phytostabilization potential. Approximately 80% of the REE was retained in the Salix ash following combustion of the biomass at 1000 °C. The findings in this research reveal that these perennial plants could be suitable candidates to control the runoff from Cd, Cr and REE affected waterbodies into freshwater resources through immobilization aligned with efficient biomass production.