The research aims at covering the mathematical modeling issues of multidimensional applied problems of ecology based on the application of a modular computing complex. The problem of modeling air pollution processes is solved by mathematical models that adequately describe fundamental processes. That reveals issues such as a detailed analysis of the atmosphere of the city or industrial area, short-term forecast of air quality in the region, assessment of long term air purification programs, optimal emission management, transboundary transfer, etc. At the same time, the formulation and methods of solving problems of environmental dynamics identification are considered, which essence is to estimate the input parameters based on the factual information about the modeled system known from the experiment. In these studies, the multidimensional equation of harmful impurities transfer was reduced to a sequence of schemes involving unknown values in a single direction, alternately in the longitudinal, transverse and vertical.The implicit schemes lead to systems of algebraic linear equations with a three-diagonal structure. Thus, the methodological basis of the difference splitting schemes provides the economic and sustainable implementation of numerical models by the scalar runs method. That approach focuses on the fact that the greatest effect of a parallel processor is achieved when it is used to perform matrix computations of linear algebra.In order to analyze the feasibility of mathematical models, a package of applications was developed to compute the transfer of harmful impurities. A solution to several applied problems for the identification of the environmental dynamics is given.