Larval drift is a critical phase of ontogeny for many species of lotic fishes. Downstream advection and dispersion of drifting larvae or eggs is controlled by the complex interaction of flow regime, channel planform, local channel morphology, and the resulting hydraulic gradients. In many regulated rivers, channel engineering and perturbations to the flow regime may disrupt natural dispersal processes and prevent successful recruitment of native fishes. Here, we explore the influence of flow regime and channel morphology on the downstream transport, dispersion, and retention of free embryos of pallid sturgeon (Scaphirhychus albus), an endangered species endemic to the Mississippi River basin and the focus of significant conservation effort on the Missouri River. The transition from drifting free embryo to exogenously feeding larvae has been identified as a potential life stage bottleneck for the pallid sturgeon. We use a two-dimensional hydrodynamic model to evaluate the sensitivity of drift and dispersion to in-channel navigation structures, constructed shallow-water habitat, and flood hydrology. In the simulations, larvae were treated as passively drifting particles and calculated retention times were used as an index of potential for settling and retention within specific environments. During low flows, retention of larvae is promoted by shallow, low velocity conditions provided by constructed side-channel habitats. At higher flows, retention is driven by overbank flows that inundate the floodplain. Based on insights gained from the analysis of field data and modeling outputs, we consider the effects of flow regime modifications or channel re-engineering on the distribution and retention of free embryos within the Lower Missouri River.