To obtain a better insight into the unsteady flow behavior in side channel pumps by a robust vortex identification method, this study presents the efficacy of the new Ω-criterion in characterizing the evolution of vortex structures in the turbulent flows under different time steps. The flow behavior and the underlying vorticity dynamics were revealed as well. Compared to Q-criterion, the new Ω-criterion identified all vortex structures irrespective of the intensity at a universal threshold of 0.52. Three different types of vortex structures (longitudinal, axial, and radial) were identified to be responsible for the turbulent flows in the side channel pumps. The beneficial longitudinal vortex promotes the momentum exchange flow between the impeller and side channel which leads to the high hydraulic head of side channel pumps. On the other hand, the unfavorable axial and radial vortex structures restricted in the impeller passage mitigate the exchange process accounting for the low efficiency of the pumps. From this study, it can be established that the evolution of the axial vortex structures is responsible for the largest vortex distribution in the impeller compared to the total vortex evolved. The impeller outer radius contributes about 60% of the unfavorable axial structures evolved. Using the new Ω-criterion, many reported anomalous findings have been explained.