Aquaculture has faced several challenges associated with the need to increase fish production (which forces an increase in farming density), as well as the presence of marine contaminants such as nanoplastics (NPs). These pollutants pose a significant risk to the sector by inducing physiological alterations that can compromise the growth and welfare of cultivated fish. Therefore, the aim of this study was to evaluate the combined effects of stocking density and dietary NP inclusion on digestive functionality in juvenile gilthead seabream (Sparus aurata). To this end, a control diet (CT) was formulated, alongside a second diet containing the same ingredients but supplemented with 5% NPs (spherical polystyrene nanoparticles, 50 nm diameter; Bang Laboratories). Both diets were administered to juveniles reared under either low-stocking-density (LSD) or high-stocking-density (HSD) conditions for 64 days. The results revealed higher activities of leucine aminopeptidase and alkaline phosphatase in the LSD-CT treatment, whereas enzyme activities were reduced at HSD regardless of dietary treatment. Conversely, enterocyte apical area was greatest in the HSD-CT group, followed by the HSD-NP group. However, microvillus height and total absorptive surface area were higher in juveniles fed the NP-supplemented diet. Collectively, dietary nanoplastic inclusion decreased intestinal enzyme activity under low-density conditions and induced adaptive ultrastructural changes to maintain digestive functionality, highlighting the need to evaluate additional parameters to fully understand the combined effects of both stressors on fish health.