Here we propose an integrative approach for comparing effects of human impacts on freshwater and terrestrial ecosystems using fundamental processes (Figures 1-3). We find several key differences in the strength and operation of these processes that suggest differing biodiversity responses in terrestrial and freshwater ecosystems (Figure 3, Table S1). For example, we find evidence suggesting that i) ecological selection due to abiotic gradients is stronger in terrestrial ecosystems than in freshwater, ii) that dispersal limitation may be greater in freshwater communities but by contrast that freshwaters have the highest potential for recovery via speciation, and iii) that the biggest data gap for cross-ecosystem comparisons is the relative influence of ecological drift among the two ecosystems. Overall, we found that quantitative comparisons across ecosystems are generally lacking, though data enabling such comparisons may be available for many organisms for the processes of dispersal and selection. In contrast, cross-ecosystem studies of speciation rates tend to focus on a few well-characterized organisms and such studies are largely missing for drift. Filling these gaps will be essential to fully link the processes of dispersal, speciation, selection and drift to the future dynamics and recovery of Earth’s biodiversity.