Understanding the damage mechanisms of composite materials requires detailed mapping of the failure behaviour using reliable techniques. This research focuses on an evaluation of the low-velocity falling weight impact damage behaviour of flax-basalt/vinyl ester (VE) hybrid composites. Incident impact energies under three different energy levels (50, 60, and 70 Joules) were employed to cause complete perforation in order to characterise different impact damage parameters, such as energy absorption characteristics, and damage modes and mechanisms. In addition, the water absorption behaviour of flax and flax basalt hybrid composites and its effects on the impact damage performance were also investigated. All the samples subjected to different incident energies were characterised using non-destructive techniques, such as scanning electron microscopy (SEM) and X-ray computed micro-tomography (πCT), to assess the damage mechanisms of studied flax/VE and flax/basalt/VE hybrid composites. The experimental results showed that the basalt hybrid system had a high impact energy and peak load compared to the flax/VE composite without hybridisation, indicating that a hybrid approach is a promising strategy for enhancing the toughness properties of natural fibre composites. The πCT and SEM images revealed that the failure modes observed for flax and flax basalt hybrid composites were a combination of matrix cracking, delamination, fibre breakage, and fibre pull out.