Quantifying the relative contributions of genetic and environmental effects and their interaction on phenotypic variation is vital to understand how populations respond to their environment. Adults can plastically respond to environmental conditions by selecting breeding and egg incubation locations that affect offspring traits during embryonic and larval development. Environmental conditions during incubation can also affect traits during later ontogenetic stages (i.e. ontogenetic contingency). Using a population of lake sturgeon (Acipenser fulvescens) from Black Lake, Michigan, we conducted field and common garden studies and evaluated whether larval phenotypes and behavior at different ontogenetic stages would vary among families whose eggs were incubated under different thermal and flow regimes in the laboratory, and associated with different micro-habitat conditions in river substrates in the field. A significant family-by-treatment interaction was detected for traits (body length, body area, head area) measured at hatch associated with different flow (high, medium, low) and temperature (10oC, 18oC, variable, ambient) treatments. The greatest range in phenotypic variance was observed among individuals reared in the most environmentally deviant conditions (warm temperature and high flow treatments). Traits measured at hatch from eggs in the stream varied due to the influences of stream micro-habitat variables, while levels of additive genetic variance covaried with age. Results demonstrate that phenotypic variation across sequential ontogenetic stages is dependent on physical stream conditions and additive genetic effects, although the relative contributions of effects differ across ontogenetic stages. Increasingly deviant environmental regimes may reveal cryptic genetic variation, potentially leading to differential survival between genotypes, thereby altering the genetic architecture of populations.