Various nanomaterials have been envisaged mainly through batch studies for environmental remediation application. The real utilization of these new generation adsorbents in large scale pose a difficulty due to its low density and small size which makes it difficult for isolation after application. In this context, nanoadsorbents polymer composite beads can be seen as a way out. Here, functionalized CNTs (carbon nanotubes) have been fabricated into micro beads with sodium alginate. The alginatefunctionalized CNT (Alg-f-CNT) beads were then comprehensively evaluated for batch and fixed-bed column separation of divalent mercury ions from an aqueous medium. The effects of process parameters such as pH, contact time, feed Hg²⁺ concentration, and temperature were studied. Simulation of the experimental data suggested that adsorption is an endothermic spontaneous process which follows the pseudo-second-order kinetic and Langmuir isotherm model. The desorption of the Hg²⁺ ion from used adsorbent was possible with 1 M HNO₃. The breakthrough curves at different process parameters were investigated during fixed-bed column separation and found to be in good agreement with Thomas model. The regeneration and reusability of the adsorbent were tested up to five cycles without a significant decrease in the removal  performance. Density functional theory studies revealed stronger interaction of Alg-f-CNT with Hg compared to free alginic acid and established the role of carboxyl and oxo groups present in the adsorbent in the coordination of the Hg²⁺ ions. The experimental results demonstrate that functionalized CNT-encapsulated alginate beads are a promising alternate material, which can be used to remove mercury in the fixed-bed column mode of the operation.