The aim of this study was to evaluate behaviour, growth, lipid composition, muscle development, and stress status of Siberian sturgeon larvae reared with two types of substrate: Bioballs1 (BB1) and Bioballs2 (BB2), when compared to no substrate (CTR). Sampling points were: hatching (T0), schooling (T1), and yolk-sac full absorption (T2). BB1 larvae were less active and showed no schooling behaviour. At T1 and at T2, BB1 larvae showed a significantly higher weight and total length than larvae reared in either CTR or BB2 (p < 0.05). The lipid content of larvae decreased over time, with little relevant differences between groups. At T2, total muscle area, slow muscle area and fast muscle area were significantly higher in larvae reared in BB1 (p < 0.05). No significant differences in muscle proliferation were found between groups. Real Time PCR was used for evaluating the relative expression of a pool of genes: myod, myog, mrf4, igf2, hsp70, hsp90a, hsp90b, and glut2. The expression of these genes did not seem to be much affected by the type of rearing substrate, except for myog and hsp70 at T1, which was greater in BB2 larvae. Our data suggest that the presence of a substrate during this developmental period seems to have positive effects but further studies would be necessary during the exogenous feeding stage.