This study appraised phyto-remediation efficiency and tolerance mechanism of Juncus effusus as was evidenced by ultra-structural modification in its roots under manganese (Mn) toxicity. Three-week-old J. effusus plants were treated with different concentrations of Mn (50, 100 and 500 µM) in hydroponics. Although higher Mn levels caused modifications in growth, biomass, height and root morphological traits, J. effusus tolerated Mn toxicity without showing any obvious phyto-toxic symptoms even under the highest level of Mn (500 µM). With incremental Mn levels in the growth media, the plants showed a steady increase in Mn uptake, while translocation factor (TF) for Mn declined. This illustrated the tendency of J. effusus plants to avoid Mn-induced stress by restricting maximum Mn in root tissues. Electron microscopy of root tip cells elucidated plant tolerance mechanism to Mn toxicity. Modification in cellular shape and size, and increased number of vacuoles and mitochondria appeared to play a major role in induction of tolerance against Mn toxicity, and ultimate survival of plant.