Globalization, specialization, and intensification have transformed the global food system, generating material flows and impacts that span multiple scales and levels, presenting novel governance challenges. Many argue for a transition toward a sustainable food system, although the scope and specific goals are fiercely contested. Theory and method is needed to evaluate competing normative claims and build legitimacy. In this dissertation Vermont serves as a case study to investigate how environmental and economic flows impact regional governance, focusing on efforts to manage agricultural phosphorus to achieve water quality goals. A material flow account is developed to estimate phosphorus flows embedded in commodities flowing in and out of Vermont⁰́₉s agricultural system from 1925-2012. The results indicate a net imbalance of phosphorus flows for the entire period, leading to the accumulation of legacy phosphorus in soils that constitutes a long-term threat to water quality. Agricultural intensification and land cover change during this period led to increased phosphorus use efficiency, livestock density, and dependency on imported feed, the largest source of phosphorus entering Vermont since the 1980s. The evidence of persistent imbalance calls into question the effectiveness of current nonpoint source pollution policy. A critical investigation of nutrient management planning policy reveals several shortcomings: pasture is frequently excluded; many phosphorus flows that cross the farm-gate are not captured; critical information on soil phosphorus levels and runoff risk is not collected in a manner that facilitates regional governance. The integration of nutrient management plans and mass-balances is proposed as an alternative approach that can increase accountability, encourage efficiency, and facilitate management and governance, albeit within constraints imposed by Vermont⁰́₉s position in a globalized market for agricultural commodities. The empirical and policy analysis is complemented by a theoretical investigation that starts from the observation that a sustainability transition inevitably entails tradeoffs amongst competing normative goals. Navigating these tradeoffs is complicated by mismatch between the reach of governance institutions and the spatial and temporal dimensions of the challenges they face. This investigation contributes to understanding how legitimacy and consensus are constructed in the context of competing normative claims and multi-level governance. It considers deliberative democracy as a means for evaluating normative claims and arriving at a shared, legitimate basis for social action. An instrumental perspective on deliberation is contrasted with a deeper notion that sees deliberation as constitutive of sustainability at a local-to-global level. A conclusion grounds this analysis by drawing out the ways in which deliberation can inform Vermont⁰́₉s efforts to govern its agriculture, water quality, and economic development, sowing the seeds for a sustainability transition.