The effects of thermal stress on survival, development and heat shock protein (hsp) expression of green sturgeon (GS) yolk-sac larvae, from hatching through yolk depletion were investigated to provide insight into effects of highly altered natural river hydrographs. Hatched GS larvae were reared at constant water temperatures 18°C (control) through 28°C at 2°C increments. Larval survival significantly decreased at 26–28°C, with 28°C being lethal. Significant proportions of deformed larvae were found at sub-lethal (20–26°C) and lethal 28°C rearing temperatures, with kyphosis (i.e. backward flexion of notochord) accounting for >99% of morphological deformities. Histological analysis of larvae preparations indicate that elevated water temperature affects notochord cell function and physiology. At rearing temperatures 20–28°C, thermal stress elicited a quick (24 h) and long lasting (yolk-sac absorption) significant over-expression of measured heat shock proteins (hsps), all of which are known components of intracellular protein repair and stabilization mechanism. Thermal sensitivity, as indicated by the incidence of abnormalities and expression of different hsps, varied significantly between crosses. Thermally tolerant progeny exhibited a short but rapid hsp72 (size in kDa) over-expression, and more pronounced hsp60 and hsp90 over-expression, than less tolerant progeny which exhibited a prolonged hsp72 and hsp78 over-expression. At environmentally relevant water temperatures bent larvae exhibited spiral swimming, which in the wild would compromise the ability of emerging larvae to forage, avoid predators, and migrate downstream, ultimately compromising survival and recruitment. Before larvae hsp content can be used as a thermal-stress biomarker for GS, field validation studies are needed.