The aim of this article is the comparative analysis of the procedures of the environmental impact assessment as well as the evaluation of the influence of construction projects on the Natura 2000 areas. The first of the procedures which precedes the issuing of the “building” decisions for construction projects that may be carried out as ones with the significant effect on the environment. The second is demanded before issuing the acceptance for developing of construction projects in the Natura 2000 areas or in their neighbourhood. Both procedures are on the critical path determining the time of preparing the construction project to carry it out. However, they show the essential differences in terms of the aim, range, methodology, subjects or responsible for their accomplishment. A bibliographical query was carried out to show the lack of generalised scheme of the impact assessment of construction projects on the Natura 2000 which makes it difficult for investors to understand it. The scheme of the sequence of actions requiered during accomplishing such assessment presented in the article was compiled with detailed description of phases and stages of “classical” environmental impact assessment may help the investor with understanding its particularities and constitutes advice when developing a detailed algorythm of dealing in a given case.