The generation of a standing wave of vortices in thin channels has been experimentally observed and discussed in the literature for the last several years. The specific cause of the wave and its response to various conditions remains largely unexplored. In this paper we model pulsatile flow through thin channels with inserted deflectors to generate the vortex wave, and we examine various measures to quantify its effects. We focus on the numerical solution of the transient vortex wave phenomenon and its response to a superimposed bulk flow, variations of pulsation, deflector spacing and shape as well as transverse suction. The quantifying measures are mapped over a Reynolds’ number–Strouhal number domain.