The effect of two environmental factors (substrate type and water velocity regime) was studied in the ontogenetic migration intensity of kaluga, Huso dauricus, a protected species in the Amur River. Early-life stages studied were: free embryos = days 0–8; larvae = days 9–49; and juveniles = days 50–66. Effect of treatments on fish migration intensity was observed in circular channels, allowing migration in an endless stream. Daily migration intensity of fish was characterized by counting the number of daily upstream or downstream fish passes past a specific site in the channel observed for 5 min every hour by vision or video camera. The hypothesis that substrate type (bare bottom or sand-small cobble) affects migration intensity was accepted, depending on the life stage. For example, the substrate type had no effect on migration intensity of days 0–6 free embryos. However, the intensity in days 7–8 free embryos and days 9–29 larvae was greater over rock substrate, while intensity in days 46–49 larvae and days 50–66 juveniles was greater when the bottom was bare. Thus, the effect of the substrate on migration varied in intensity according to the life stage, and within the larva life stage, by age. The velocity regime had a positive effect on migration intensity of free embryos, but a high velocity (mean, 29.9 cm∙s−1) delayed the resting period of day 8 free embryos and day 9–15 larvae. Free embryos and larvae in low vs fast velocities showed that they may have a drive to migrate a similar distance, and moreover, that a triggering velocity may be needed to initiate or to stop migration. The hypothesis was accepted that the rearing velocity affects migration intensity, e.g. larvae reared in still water and then placed in moving water had a compensatory migration intensity response. For population enhancement stocking of H. dauricus, the results indicate culture practices must insure that: (i) same-population individuals are mated to produce early-life stages with the correct behaviour, (ii) migrating larvae, not juveniles, should be stocked, and (iii) larvae should be released in a river reach with a bottom velocity ≥30 cm∙s−1 containing sand and small pebbles.