In this paper we incorporate the interdisciplinary New Institutional and Transaction Costs Economics (combining Economics, Organization, Law, Sociology, Behavioral and Political Sciences), and suggest a framework for analyzing the mechanisms of governance of sustainable development. The agricultural sector is used to illustrate the approach, test the framework, and support with examples. Firstly, we discuss the modern concepts and the economics of sustainability. Secondly, we present a new framework for analysis and improvement of the governance of sustainable development. This new approach takes into account the role of specific institutional environment; and the behavioral characteristics of individual agents; and the transaction costs associated with the various forms of governance; and the critical factors of economic activity and exchanges; and the comparative efficiency of market, private, public and hybrid modes; and the potential of production structures for adaptation; and the comparative efficiency of alternative modes for public intervention. Finally, we identify specific modes for environmental governance in Bulgarian agriculture; and access the efficiency of market, private and public modes; and estimate the prospects for evolution of environmental governance in the conditions of EU CAP implementation. Agrarian development is associated with specific (different from other European states) environmental challenges such as degradation and contamination of farmland, pollution of surface and ground waters, loss of biodiversity, significant greenhouse gas emissions etc. That is a result of the specific institutional and governing structure evolving in the sector during the past 20 years. Implementation of the common EU policies will have unlike results in “Bulgarian” conditions enlarging income, technological, social and environmental discrepancy between different farms, sub-sectors and regions. Dominating subsistence farming, production cooperatives, small-scale commercial farms, and large business firms will be highly sustainable in years to come.