Natural ecosystems are shaped along two fundamental axes, space and time, but how biodiversity is partitioned along both axes is not well understood. Here, we show that the relationship between temporal and spatial biodiversity patterns can vary predictably according to habitat characteristics. By quantifying seasonal and annual changes in larval dragonfly communities across a natural predation gradient we demonstrate that variation in the identity of top predator species is associated with systematic differences in spatio-temporal β-diversity patterns, leading to consistent differences in relative partitioning of biodiversity between time and space across habitats. As the size of top predators increased (from invertebrates to fish) habitats showed lower species turnover across sites and years, but relatively larger seasonal turnover within a site, which ultimately shifted the relative partitioning of biodiversity across time and space. These results extend community assembly theory by identifying common mechanisms that link spatial and temporal patterns of β-diversity.