This work studies the nitrate removal efficiency in porous media using nanoscale zero valent iron (nZVI) and modified surface of nZVI using Cu metal (known as bimetallic nano-Fe/Cu particles) in a multilayer system through an upflow packed sand column. The effect of multilayer and different thicknesses of nZVI/sand and nano-Fe/Cu particles on the nitrate removal performance was investigated. 10 g of nZVI and nano-Fe/Cu particles were introduced in each column with different layers configuration. The initial nitrate concentration was 45 NO3--N mg/L. The distribution of nitrate trapped inside the column was evaluated by measuring nitrate concentrations, not only at the column inlet and outlet, but also at various intermediate sampling ports along the depth of the column. The results showed that the best condition to remove nitrate among nZVI/sand columns was observed when using a single 10-cm high layer of nZVI/sand and more than 97% of influent nitrate was removed. Whereas in (nano-Fe/Cu)/sand columns, the optimum performance was noted when using double 5-cm high layers of (nano-Fe/Cu)/sand and a complete removal was attained (100%). Furthermore, nano-Fe/Cu particles showed better removal efficiency than nZVI for the treatment of nitrate in simulated groundwater. Based on the results obtained, it was concluded that using nZVI in the full length of porous media or using nano-Fe/Cu particles in multilayer porous media could enhance nitrate removal effectively.