Magnetic Fe3O4 assembled on nanoscale zero-valent iron (nZVI) supported on an activated carbon fiber (ACF) to form nanoscale magnetic composites (nZVI-Fe3O4/ACF) for removing Cr(VI) and Cu(II) from aqueous solution through a permeable reactive column was synthesized via an in situ reduction method. The nZVI-Fe3O4/ACF composites and the interaction between nZVI-Fe3O4/ACF and both Cr and Cu ions were characterized by field emission scanning electron microscopy (FESEM) with EDX, TEM, XRD, and XPS. Batch experiments were used to analyze the effects of main factors on Cr(VI) removal and investigate the simultaneous removal of Cr(VI) and Cu(II) through a permeable reactive column. The results indicated that the ACF and Fe3O4 can inhibit the agglomeration and enhance the dispersibility of nZVI, and Fe3O4 and nZVI displayed good synergetic effects. The removal efficiency of Cr(VI) improved with the increase amount of Fe3O4 in the nZVI-Fe3O4/ACF composites. With low initial concentration of Cr(VI) and acidic conditions, ~ 90% of 20.0 mg·L−1 Cr(VI) in the solution was removed after 60 min. The removal of Cr(VI) was also affected by coexisting ions. The removal efficiency of 10.0 mg·L−1 Cu(II) was ~ 100% after 45 min of reaction, and the presence of Cu(II) can accelerate the reduction of Cr(VI). The simultaneous removal mechanisms of Cr(VI) and Cu(II) by the nZVI-Fe3O4/ACF composites also were proposed.