The present ecological situation and negative influence of ecological factors on public health in the Russian Federation are analysed in this article. Russia is one of the most polluted countries in the world, and the environmental problem is very important here. In spite of some decrease in pollution during the crisis period, nature does not have time to neutralize pollution accumulated before, and as a result, there is an increase in the pollution concentration. In 66 cities (40 million people) with excess 10 times and more than permitted maximum concentration level, the morbidity is above the average Russian level of 1.6 - 2 times. The forecast of emission according to the various scenarios of Russian development has been done: a pessimistic scenario with a slowdown in economic growth and an optimistic scenario with the acceleration of economic growth. The optimistic scenario is realized under the hypothesis about the oil prices increase and the real rouble exchange rate strengthening at the end of 2015, the revival of investment processes, the successful policy of import substitution, and the competent using of the instruments of monetary and fiscal policy. The pessimistic scenario is implemented under the assumption of negative economic tendency prolongation of 2014. For the forecast analysis, the dynamic inter-industry model with the ecological block was used. At the optimistic scenario implementation, the additional burden on the natural environment should be expected. The most important result of the research is the estimation of the rates of ecological payments which are necessary for performing the functions stimulating the environmental protection activity. The article presents the findings about the need to improve the institutional ecological structures, the scientific basis of pollution taxes, the introductions of the stimulating tools of the economic nature protection mechanism. The results presented in the article may be used both in elaborating the eco-economic forecasts of the development of Russia and as the information and analytical recommendations in developing the directions of the state and regional nature protection policy.