A vital component of spiral-wound membrane modules is the spacer mesh. It not only structurally supports the membranes but also aids in mass-transport enhancement through the membrane surface. Fundamental understanding of hydrodynamics associated with these spacer designs is critical to improve the permeate flux performance by decreasing concentration polarization and minimizing (bio)fouling, as well as minimizing the axial pressure drop. In the present study, time and space resolved Direct Numerical Simulations (DNS) were performed for a commercial spacer geometry. The spacer geometry was reconstructed by measurements using Scanning Electron Microscopy (SEM). Computations were performed for three spacer cells, allowing elimination of stream-wise periodicity that was a major bottleneck in earlier studies. The numerical solver was well checked in terms of boundary layer profiles obtained from Particle Image Velocimetry (PIV) data and with pressure measurements corresponding to various flow channel velocities. Non-dimensional computations were performed for Reynolds Numbers (Re) ranging from 73 to 375 (inlet channel velocity of 0.073–0.375 m/s) covering the flow transition dynamics regime. Results indicate that flow transition from steady to unsteady regime occurs for Re > 250. The flow transition could be primarily attributed to the interaction between vortices attached to the spacer filaments and the screw-vortex that originates along the diagonal of the spacer cells. No turbulent transition was observed even at the highest investigated velocity (Re = 375). The frequency spectra of time-varying velocity signal shows that at Re > 350 a sudden shift of frequency spectra occurs from discrete to continuous mode indicating the onset of advanced instability. Spacer design criteria in terms of maximum principal stress is also proposed, which can potentially aid in minimizing biofilm seeding.