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Sustainability of water use in the Arctic zone of big rivers is growing in importance. Water is a renewable natural resource, so the main task of water use is to maintain this renewability. A fractal approach is one of the promising ways to the description of non-equilibrium aquatic ecosystems under the conditions of their host territories urbanization. This approach used to assess the sustainability of water use in the Arctic zone of the Yenisei River basin shows that the features of the economic use and the management of the development of water bodies should be of a preventive nature and be reduced to the management of potential anthropogenic risks. The ecosystem cannot independently compensate the negative impact of anthropogenic load components. As a result, the techno-natural balance is disturbed, and the probability of ecosystem destruction is growing rapidly. Environmental risks of economic water use arise if an ecosystem development is not supported by the conservation of its biological resource, i.e. the limiting cycle of ecosystem adaptation to external anthropogenic load is violated. The fractal approach opens up new possibilities for predicting the stability of water bodies based on the results of standard environmental monitoring of surface water pollution. It is important that such a forecast is based on the calculation of the fractal index of a water body stability, which is directly related to the maximum permissible environmental load (MPEL) as a marker of the maximum technological capacity of urban ecosystems.