Abstract

Biogeochemistry has traditionally been grounded in a substance-based ontology, modeling ecosystem dynamics through discrete nutrient pools and linear fluxes. While such frameworks have advanced our understanding of carbon, methane, and phosphorus cycling, they often obscure the dynamic, relational, and emergent character of biogeochemical processes. This paper introduces a process-ontological framework for biogeochemistry that reconceptualizes elemental transformations not as state transitions between static compartments but as evolving networks of interdependent processes. Drawing on process philosophy, complexity theory, and resilience science, we articulate four foundational principles (relationality, scale dependence, temporal continuity, and emergence) that underpin a processual understanding of biogeochemical systems. Through empirical cases focused on methane and phosphorus cycling, we demonstrate how process ontology informs both modeling strategies and governance practices, including the detection of early warning signals, policy design, and cross-scale management of tipping points. Rather than replacing substance-based approaches, this framework complements them, revealing their underlying metaphysical assumptions and situating them within a broader ontology of dynamic interdependence. It also emphasizes the epistemic–ontological reciprocity of scientific practice, in which conceptual frameworks and empirical observation iteratively refine one another. By embedding ontological reflection within empirical and governance contexts, this work contributes to a broader rethinking of how scientific models mediate between conceptual frameworks and ecological realities, supporting adaptive, transformative and process-aware strategies for environmental management.