The eddy structures and their mutual interactions in a three-dimensional channel with a backward-facing step for the transitional Reynolds number 900 were investigated numerically. The aim was to reveal the structural development of the entire vortical flow field, which could immensely enhance the knowledge about vortical structures occurring in the recirculation region near the step wall. Simulations were made to reproduce the experimental observations and provide clear indications about the strong interaction between the shear layer instabilities. Physical instabilities of this type were amplified by the shedding-type instabilities and induced by the interaction of coherent structures with the sidewalls of the duct. These interactions were responsible for the flapping motion of interior shear layer. Careful attempts were made to reveal the behaviour of these vortical structures by means of vortex stretching, roll-up of vortex lines and formation of vortex tubes. Also, the three-dimensional flow topology of the velocity field corresponding to stationary helical vortex (SHV) was analysed extensively. The SHV flow consisted of a pair of counter-rotating helical cells in a double helix structure wrapped around the vortex tube. The roll-up shear-layer hovering vortices were observed near the step to initiate the Kelvin–Helmholtz-like instability. The Kelvin–Helmholtz vortices were developed into lambda-shaped vortices which impinged on the step-wall and were elongated into the hairpin-like vortices.