Motile and driven particles confined in microfluidic channels exhibit interesting emergent behavior from propagating density bands to density shock waves. A deeper understanding of the physical mechanisms responsible for these emergent structures is relevant to a number of physical and biomedical applications. Here, we study the formation of density shock waves in the context of an idealized model of microswimmers confined in a narrow channel and subject to a uniform external flow. Interestingly, these density shock waves exhibit a transition from 'subsonic' with compression at the back to 'supersonic' with compression at the front of the population as the intensity of the external flow increases. This behavior is the result of a non-trivial interplay between hydrodynamic interactions and geometric confinement, and is confirmed by a novel quasilinear wave model that properly captures the dependence of the shock formation on the external flow. These findings can be used to guide the development of novel mechanisms for controlling the emergent density distribution and average population speed, with potentially profound implications on various processes in industry and biotechnology such as the transport and sorting of cells in flow channels. , and pathogens in the urinary tract [6]. The ability to control the density distribution and group velocity of micro-particles in flow would therefore have numerous applications in physics and biology. This letter analyzes, via discrete particle simulations and macroscopic models, the emergent patterns in populations of motile particles driven by an external flow in a rectangular micro-channel.The dynamics of single and many-swimmer systems are typically studied in unconfined settings [7][8][9]. The effects of confinement to narrow flow channels are less well understood; see, e.g., [10][11][12][13][14] and references therein. Recent experiments on driven droplets [3,[15][16][17] and self-propelled colloids [18,19] in quasi two-dimensional (Hele-Shaw type) channels show the emergence of traveling density waves, including density shocks at the wave front. Similar observations are reported in simulations of confined self-propelled particles [20], albeit with density shocks forming at the back of the wave. The primary mechanism responsible for the emergence of these density waves is attributed to hydrodynamic interactions (HI) among the confined particles [18,20]. Confinement in Hele-Shaw type geometries induces a distinct hydrodynamic signature; the particle far-field disturbance is that of a source dipole irrespective of the details of the particle transport mechanism, driven or self-propelled, pusher or puller [3,15,16,21,22]. Additional confinement to a narrow channel does not alter the nature of hydrodynamic interactions but imposes impenetrability conditions on the lateral boundaries of the channel. These effects are properly accounted for in the model used in [20], and, * corresponding author: kanso@usc.edu thus, do not explain the discrepancy in the location of the shock ...