The paper considers a methodology of mathematical modeling ofecological-economicprocesses at the regional level. The basis of the model is formed by equations,which describetwo interacting blocks: economic and ecological ones. Equations of the economicblock are representedby relations of generalized inter-branch balance, while the ecological part isdescribedin terms of differential equations with deviations with respect to some givenstate of natural resources.Issues of i) information support of the model, ii) techniques used foridentification of thecoefficients, iii) scenario analysis and iv) forecasting are analyzed.