Little information is available on governing factors of larval fish dispersal in natural river systems. Therefore, we aimed to describe dispersal and retention of marked larval nase carp, Chondrostoma nasus, along a shoreline nursery habitat of the River Danube. Based on a three-dimensional hydrodynamic model, we analyzed the influence of the hydraulic conditions on larval dispersal. We also related observed larval pathways to numerical particle tracing. Clear differences in the temporal drift pattern were due to significant differences in the hydrodynamic characteristics of the release stations. Some larvae remained in the study reach, most upstream of the release point. These were significantly larger than drifting larvae. We conclude that larval dispersal has an active component and that dispersal and retention patterns are dependent on the habitat structure and hydrodynamic characteristics of the releasing points. This emphasizes the importance of links between the location of spawning sites within the river and variation in flow during early development, the combination of which may contribute to successful recruitment of fluvial fish species.