Relationships between biodiversity and ecosystem functioning (BEF) are typically investigated separately in different ecosystem types, often neglecting connections across ecosystem boundaries. Here, we examined the cross-boundary relationships between terrestrial and aquatic biodiversity and terrestrial and aquatic ecosystem function (here productivity in terms of biomass). We collected a dataset from 100 Finnish boreal lakes for phytoplankton and zooplankton, and for trees and understory plants in the surrounding forest ecosystems. We explored the connections among climatic, catchment, and local environmental factors, and terrestrial and aquatic biodiversity and productivity using structural equation modeling (SEM). The results indicated cross-boundary connections between the two realms. Terrestrial biodiversity was associated with terrestrial productivity and connected to lake water chemistry directly and indirectly through terrestrial productivity. Water chemistry in turn was linked to aquatic biodiversity and productivity. Within both realms, biodiversity was positively associated with ecosystem productivity. The effects of biodiversity per se were weaker in the aquatic realm, in which nutrient availability was the strongest determinant of productivity. Our findings underscore the importance of exploring cross-ecosystem coupling, as the impacts of several global change drivers, such as climate and land-use change or eutrophication extend beyond individual realms to transcend ecosystem boundaries. In particular, the combined effects of warming, eutrophication, and increasing terrestrial productivity are likely to increase the import of allochthonous nutrients to boreal lake ecosystems, resulting in enhanced primary productivity therein. As freshwater ecosystems integrate the effects of direct and indirect changes in their catchments, they serve as ideal settings for investigating cross-ecosystem coupling and act as valuable sentinels of climate and other global changes.