The aim of the project was to develop a methodology to assess state of the environment and its prediction in the form of evaluation of material and energy flows of systems, including obvious and hidden flows, and further to process a pilot project on the basis of the proposed methodology in specific conditions of our state, at the level of a company and a region. Furthermore, methodology for measuring material flows was also proposed at the level of the entire Czech Republic. This methodology was based on overview of analyses of major methodologies commonly used for assessing state of the environment in USA, Japan, Germany, the Netherlands, and at a company level in EU states, Austria and Sweden. The proposal of methodology for the Czech Republic is the basis for research of reduction of total environmental costs, reduction of impacts and effects of human activities on the environment, and the information background contributing to regulations of these effects.