From microorganisms to the largest macroorganisms, much of Earth’s biodiversity is subject to forces of physical turnover. Residence time is the ratio of an ecosystem’s size to its rate of flow and provides a means for understanding the influence of physical turnover on biological systems. Despite its use across scientific disciplines, residence time has not been integrated into the broader understanding of biodiversity, life history, and the assembly of ecological communities. Here, we propose a residence time theory for the growth, activity, abundance, and diversity of traits and taxa in complex ecological systems. Using thousands of stochastic individual-based models to simulate energetically constrained life history processes, we show that our predictions are conceptually sound, mutually compatible, and support ecological relationships that underpin much of biodiversity theory. We discuss the importance of residence time across the ecological hierarchy and propose how residence time can be integrated into theories ranging from population genetics to macroecology.