Glycerol is a 3-carbon sugar alcohol successfully employed as an alternative feed ingredient for land-farmed animals and more recently for farmed fish. While most studies address zootechnical performance, few have delved into the metabolic utilization of dietary glycerol. A growth trial was performed using diets with increasing levels of glycerol (0, 2.5 and 5%) on two relevant species for aquaculture: rainbow trout (8-week trial; 3 tank per diet/25 fish per tank, on a 15 ± 1°C flow-through freshwater system); and European seabass (6-week trial; 5 tank per diet/6-8 fish per tank on a 21°C indoor saltwater RAS system). After this period, fish were subjected to a metabolic trial consisting of a 6-day residence in deuterated water (2H2O). Measurements of blood glucose and hepatic glycogen 2H-enrichments through Nuclear Magnetic Resonance, complemented by mRNA levels of key-enzymes for intermediary metabolism were used to evaluate the catabolic pathways of dietary glycerol. Dietary glycerol had no impact on plasma glucose, but hepatic glycogen levels increased significantly with increasing dietary glycerol levels in both species. While trout was able to regulate circulating glycerol plasma, seabass presented elevated levels on the glycerol-supplemented diets. Despite revealing some significant differences between sampling time (6 and 24 h), none of the enzymes’ mRNA levels responded to the dietary treatment. In trout, the main source of blood glucose was not labeled with 2H (~60%, likely from diet) while other contributors did not differ with glycerol supplementation. In seabass, the unlabeled contribution was approximately half of that observed in trout (~30%), accompanied by a significant increase of gluconeogenic contributions at the triose-phosphate level to the blood glucose with increasing dietary glycerol. In trout, labeling from 2H2O into hepatic glycogen revealed significant differences, with the contribution from the indirect pathway at the triose-phosphate level increasing with increased dietary glycerol. No such differences were found in seabass’ glycogen pool. These findings suggest that fish species are able to retain, catabolize glycerol and incorporate it into carbohydrates. The gluconeogenic utilization of exogenous glycerol differed between species and affected the synthesis of hepatic glycogen in trout and the appearance of blood glucose in seabass.