Additive manufacturing (AM) is an advanced manufacturing method that produces objects by sequential layering. Material extrusion AM (MEAM) with continuous-fibre reinforcement is becoming more widely used in naval structures, which are exposed to the marine environment. However, the water diffusion process and the effect of water ageing on the mechanical performance of AM materials are not yet well understood because of their complex internal structure, caused by defects generated during manufacturing. Current research on diffusion is mostly based on experimental methods for conventionally manufactured materials without considering AM-induced defects. The objective of this study is to explore how the defects inherent to MEAM affect water diffusion in a composite material by the capillary effect. Results from a numerical study of capillary flow in MEAM polymer are applied as a boundary condition in the subsequent finite-element analysis. The study illustrates that flow in the capillary reaches the steady state quicker compared to the saturation time in the matrix, predicted by Fick’s diffusion equation. It is demonstrated that the capillary effect can significantly affect the water diffusion in MEAM parts and reduce the saturation time to one-third compared to the case without accounting for this effect.