In substrate-limited systems, oyster reef restoration can be improved by a greater understanding of the role of complexity in substrate design. Here, we tested different substrate designs with the aim to determine whether substrate morphology, complexity or local hydrodynamics was most important for Saccostrea glomerata recruitment. Photogrammetry was performed at oyster reefs in New South Wales to create a 3D model. A subsection of this model was used to 3D print a nature-inspired substrate tile that resembled the morphology of the Sydney rock oyster reef. A tile with similar complexity to the nature-inspired tile was created by filtering out the oyster related roughness to a design that had a comparable kt (total roughness) value. Computational Fluid Dynamic modelling was used to determine the bed velocity across the nature-inspired tile and this velocity was matched in a hydrodynamically similar tile. These three tiles and a flat control were deployed in the field for two months at two different estuaries to test oyster recruitment. All three tiles significantly outperformed the flat control tile, while the nature-inspired and complexity-similar tile exhibited morphologically driven clustering effects on recruitment. Untangling the mechanisms driving oyster recruitment can assist in substrate design for future restoration projects.