The influence of three different initial stocking densities (low stocking density [LSD] = 1.5 kg/m2; medium stocking density [MSD] = 3 kg/m2; and high stocking density [HSD] = 6 kg/m2) in flow‐through systems was evaluated on growth and welfare in beluga, Huso huso, and ship sturgeon, Acipenser nudiventris, juveniles for 2 mo. Fish were kept in 18 concrete square tanks (2.0 × 1.0 × 1.2 m3) at 22.3 ± 0.4 C and under a natural photoperiod. In both species, the growth performance in terms of final body weight, weight gain, specific growth rate, and feed intake significantly decreased with increasing stocking density (P < 0.05). In both species, the percent of neutrophils increased after 60 d of trial (P < 0.05). Moreover, hematocrit and white blood cell counts increased after 60 d of trial in ship sturgeon (P < 0.05). Plasma immunoglobulin significantly decreased with increasing stocking density in both species. Plasma insulin‐like growth factor I decreased with increasing stocking density in beluga; however, it was not affected in ship sturgeon. Overall, these results showed that the LSD group in both species demonstrated more homogeneous and higher growth rate than the MSD and HSD groups.