Human impacts such as habitat loss, climate change and biological invasions are radically altering biodiversity, with even greater effects projected into the future. Evidence suggests human impacts may differ substantially between terrestrial and freshwater ecosystems, but the reasons for these differences are poorly understood. We propose an integrative approach to explain these differences by linking impacts to the fundamental processes that structure communities: dispersal, speciation, ecological selection and ecological drift. Our goal is to provide process-based insights into why human impacts, and the responses to these impacts, may differ across ecosystem types within a mechanistic, eco-evolutionary comparative framework. To enable these insights, we review and synthesize i) how the four processes can influence diversity and dynamics in terrestrial and freshwater communities, focusing on whether their relative importance may or may not differ among ecosystems, and ii) how human impacts can alter terrestrial and freshwater biodiversity in different ways due to differences in process strength among ecosystems. Finally, we highlight research gaps and next steps, and discuss how this approach can provide new insights for conservation. By focusing on the processes that shape diversity in communities, we aim to mechanistically link human impacts to ongoing and future changes in ecosystems.