Paper presents generalized approach and shows universal methodology how to use computer algebra based systems (CAS) for the implementation of mathematical models with formula and data uncertainties. Various approaches for solving uncertainty with the computer algebra system Maple are presented. The modified model COPERT III with included uncertainty was developed in Maple and some results of the case study for the transport influence and all the related air pollution in the Czech Republic are presented together with the case study devoted to the assessment of waste management indicators in South Moravia region.