This article outlines an original approach to analyzing the development of the system of spatial nature conservation, and the system itself is shown as a distinctive phenomenon of natural, socio-cultural and economic genesis. Emphasis is placed on institutional, structural and material changes within systems characterized by a set of factors, actors, trajectories and vectors. The factors include the conditions that ensure the availability of resources for the emergence and existence of protected ecosystems. They also determine the current state and trends of the nature protection system determining the current status and tendencies for change of the nature conservation system. Especially protected natural areas, their networks and environmental legislations were used as active agents of the transformations. It is suggested that the elementary changes should be described by means of trajectories which are generalized into transformation vectors, which indicate the possible changes in nature conservation systems. Application of these authors’ hypothesis is illustrated by the example of 540 nature conservation sites, nature conservation systems and legislation of nine regions of Western Siberia. The analysis revealed signs of a crisis situation in the national system of nature conservation. It is established that the regional systems constitute a key element in the structure of the country’s environmental organization, and the direction and synchronicity of the development vectors within and between them determine the prospects for higher-rank environmental networks. It is concluded that there is a need for the synchronization of regional legislative processes in line with the traditional national foundations of reserve management and studies.Keywords: spatial nature conservation, specially protected natural areas, trajectories and vectors of changes, reserve management and studies.