The sustainable composition of diets of high nutritional value is of the utmost importance for intensive aquaculture. Digestion and absorption of nutrients depends on the activity of the digestive enzymes, in particular those located in the brush border membrane of enterocytes, which are responsible for the final stages of breaking down and absorption of nutrients. In the present study, the substitution of fish meal by lupin or rapeseed meal in the diet was evaluated on gilthead sea bream (Sparus aurata) and goldfish (Carassius auratus). The objectives were to compare the activities of intestinal brush border enzymes in both species fed the control and experimental diets. When gilthead sea bream were fed the vegetable diets, significantly lower activities compared to the control group were observed for alkaline phosphatase and γ-glutamyl transpeptidase, but these differences were not significant in goldfish. Maltase activity was found decreased in the group fed lupin meal, both in sea bream and in goldfish. However, in spite of these differences in enzyme activities, growth characteristics of the fishes were similar with the three diets. It seemed that both fish were able to adapt to partial substitution of fishmeal, but it remains to investigate the mechanism for compensating the decrease in specific enzymatic activity in the enterocytes of carnivorous gilthead sea bream.