Land-based aquaculture facilities experience occasional hypercapnic conditions due to the accumulation of the metabolic waste product carbon dioxide. Pre-gonadal Lytechinus variegatus (horizontal diameter = 20 mm) were exposed to control (608 μatm pCO2, pH 8.1) or hypercapnic conditions (1738 μatm pCO2, pH 7.7) in synthetic seawater for 14 weeks. Sea urchins exposed to hypercapnic conditions exhibited significantly slower growth (reduced dry matter production), primarily due to reduced test production. Higher fecal production rates and lower ash absorption efficiency (%) in individuals exposed to hypercapnic conditions suggest the ability to process or retain dietary carbonates may have been affected. Significant increases in neutral lipid storage in the gut and increased soluble protein storage in the gonads of individuals exposed to hypercapnic conditions suggest alterations in nutrient metabolism and storage. Furthermore, organic production and energy allocation increased in the lantern of those individuals exposed to hypercapnic conditions. These results suggest chronic exposure to hypercapnic conditions alters nutrient allocation to organ systems and functions, leading to changes in somatic and reproductive production. © 2014 © 2014 Taylor & Francis.