It must be noted that development of such a diversified mineral base is often restricted due to environmental and landscape protection constraints, the need to protect underground waters, presence of technical infrastructure and ownership rights to the land where a deposit is documented (Radwanek-Bąk 2008, 2009). The influence of mining on biological diversity is of particular concern, as exploitation of mineral deposits can have many adverse effects such as deterioration, disruption or even destruction of habitats, interference with functioning of species and their relocation. The scope of the interference caused by a mine in each case is individual and depends on numerous factors. These can be the mineral type, the size of a mine, mining technology used, as well as the sensitivity of the environment where the mining takes place. With the aim to protect the scarcest and most endangered species and habitats, the Nature 2000 network has been established in the European Union. These areas do not always prohibit mining of non-energy minerals (within this rock minerals) but must be carried in accordance with UE directives (habitat and bird) (NEEI, 2010). The paper presents the concept and development methodology of a geo-information system designed for optimisation of rock minerals management on the regional scale.