This article presents the rationale for the need to take into account and assess natural capital as an important factor for viable managerial decision-making concerning the study, use and reproduction of natural resources in the interests of sustainable development. The activity of authorities in Tomsk oblast was used as an example in examining the issues related to taking into account and assessing natural capital and ecosystem services into the system of managerial decision-making. We used strategic and normative documents of Tomsk oblast, departmental information and material from previous research into assessments of natural capital. A rationale is given for the need to improve the institutional conditions for proper inventory and assessment of all functions of natural capital and ecosystems in managerial decision-making, namely the development of the monitoring system for economic value in the sphere of environmental management which is based on the system of ecological-economic accounting and constitutes a set of coherent statistical indicators reflecting the status of natural capital. The mechanism is suggested for generation of the information-methodological base of economic assessment of natural capital. It is determined that a qualitatively new information basis integrated into the system of regional management. Qualitatively new information basis integrated into the regional government system will make it possible not to simply obtain information on the flows of expenditures and benefits in the sphere of environmental management, but also to ensure interaction between state and municipal authorities and with organizations and the population. The monitoring system for economic value of natural capital and ecosystem services integrated into the region’s executive bodies will permit adaptive governance of environmental management of the region in the face of changes and uncertainty.Keywords: sustainable development, natural capital, ecosystem services, economic assessment, environmental management.