The three-dimensional architecture of natural habitats is a key determinant of species biodiversity, harvestable biomass and resilience to disturbance1,2. Indeed, some species, including trees, corals and oysters, alter resource availability and modify biotic and abiotic pressures through their own three-dimensional structures—thereby enhancing their own survival3,4. However, which aspects of the three-dimensional architecture of these ecosystem engineers shape ecosystem dynamics and species survival are rarely examined by empirical studies, leaving much of the broader ecological and conservation impact of ecosystem engineering underexplored4–6. Here we show that oyster reefs have combinations of geometric variables that maximize recruit survival, which is a key factor influencing oyster reef growth and persistence. Using three-dimensional habitat designs that capture the full spectrum of natural oyster reef architectures, as well as a geometric theory7 that links habitat surface area, fractal dimension and height, we show that oyster settlement and survival are greatest at particular combinations of fractal dimension and height that minimize predation. Our study provides a template for understanding optimal three-dimensional habitat configurations for habitat restoration projects that are proliferating globally, without targeting key architectural features of habitat space that maximize restoration success8,9.
