Current design of bioretention systems is intended to intercept and retain stormwater, enhance infiltration, and remove organic particulates, nutrients, pathogens, metals, and other contaminants using natural processes that derive from the interactions of water, soil, microbes, plants, and animals. Most bioretention systems function as isolated patches of various shapes and sizes surrounded by impervious surface. A significant body of ecological theory has been developed that addresses the relationships among species composition, diversity, and ecosystem function, and how these vary with spatial structure. Here we highlight how such theories may be applied to improve the efficiency or effectiveness of bioretention systems. We consider (1) the role of plant and animal species that function as ecosystem engineers, (2) biodiversity–ecosystem function relationships, (3) complexity and stability, (4) disturbance and succession, and (5) spatial theory. Future testing of the utility of these theories may occur through incorporation of experiments into the design of bioretention systems or through meta‐analysis of systems that span a range of configurations and biotic features. WIREs Water 2015, 2:259–270. doi: 10.1002/wat2.1072This article is categorized under: Water and Life > Conservation, Management, and Awareness Engineering Water > Sustainable Engineering of Water Science of Water > Water Quality