The transition from drifting free embryo to exogenously feeding larvae has been identified as a potential life-stage bottleneck for the endangered Missouri River pallid sturgeon. Previous studies have indicated that river regulation and fragmentation may contribute to the mortality of larval pallid sturgeon by reducing the extent of free-flowing river available to free embryos to complete ontogenetic development. Calculations of total drift distance based on mean velocity, however, do not address the potential for complex channels and flow patterns to increase retention or longitudinal dispersion of free embryos. We use a one-dimensional advection–dispersion model to estimate total drift distance and employ the longitudinal dispersion coefficient as a metric to quantify the tendency towards dispersion or retention of passively drifting larvae. We describe the effects of different styles of channel morphology on larval dispersion and consider the implications of flow regime modifications on retention of free embryos within the Lower Missouri River. The results illustrate the complex interactions of local morphology, engineered structures, and hydraulics that determine patterns of dispersion in riverine environments and inform how changes to channel morphology and flow regime may alter dispersion of drifting organisms.