Natural fibre-reinforced composites (NFCs) have attracted attention as sustainable alternatives to synthetic fibre composites. However, their hydrophilic nature and susceptibility to moisture absorption, especially in combination with process-related defects, can compromise long-term performance. This study critically examines the effects of hydrophobic fumed silica, incorporated into an epoxy matrix, on the processing, moisture uptake, and mechanical properties of flax/epoxy laminates produced via resin transfer moulding (RTM). Epoxy systems containing 0–5 wt% silica were characterised in terms of particle dispersion, rheological properties, thermal behaviour, and water absorption. Corresponding laminates were analysed for void content, Fickian diffusion behaviour, and tensile performance in dry and saturated states. Despite its hydrophobic surface treatment, silica increased resin water uptake and, at 5 wt%, led to a substantial rise in viscosity, poor fibre impregnation, and increased porosity. The resulting laminates exhibited faster and higher moisture uptake and significantly reduced wet mechanical properties, especially for highly filled systems. While thermal stability improved slightly, the overall findings revealed that the chosen silica-based matrix modification led to clear trade-offs and processing limitations under RTM conditions. This study highlights the importance of assessing such limitations early in the design process and demonstrates that the selected silica type is not a viable strategy for improving moisture resistance in NFCs.