The biodiversity–ecosystem functioning concept asserts that processes in ecosystems are markedly influenced by species richness and other facets of biodiversity. However, biodiversity–ecosystem functioning studies have been largely restricted to single ecosystems, ignoring the importance of functional links – such as the exchange of matter, energy, and organisms – between coupled ecosystems. Here we present a basic concept and outline three pathways of cross-boundary biodiversity effects on ecosystem processes and propose an agenda to assess such effects, focusing on terrestrial–aquatic linkages to illustrate the case. This cross-boundary perspective of biodiversity–ecosystem functioning relationships presents a promising frontier for biodiversity and ecosystem science with repercussions for the conservation, restoration, and management of biodiversity and ecosystems from local to landscape scales.