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Critical Zone Science (CZS) represents a powerful confluence of research agendas, tools, and techniques for examining the complex interactions between biotic and abiotic factors located at the interface of the Earth's surface and shallow subsurface. Earth's Critical Zone houses and sustains terrestrial life, and its interacting subsystems drive macroecological patterns and processes at a variety of spatial scales. Despite the analytical power of CZS to understand and characterize complicated rate-dependent processes, CZS has done less to capture the effects of disturbance and anthropogenic influences on Critical Zone processes, although some Critical Zone Observatories focus on disturbance and regeneration. Methodological approaches from biogeography and ecology show promise for providing Critical Zone researchers with tools for incorporating the effects of ecological and anthropogenic disturbance into fine-grained studies of important Earth processes. Similarly, mechanistic insights from CZS can inform biogeographical and ecological interpretations of pattern and process that operate over extensive spatial and temporal scales. In this paper, we illustrate the potential for productive nexus opportunities between CZS, biogeography, and ecology through use of an integrated model of energy and mass flow through various subsystems of the Earth's Critical Zone. As human-induced effects on biotic and abiotic components of global ecosystems accelerate in the Anthropocene, we argue that the long temporal and broad spatial scales traditionally studied in biogeography can be constructively combined with the quantifiable processes of energy and mass transfer through the Critical Zone to answer pressing questions about future trajectories of land cover change, post-disturbance recovery, climate change impacts, and urban hydrology and ecology.