The aim of the article was to identify changes in the structure of land use and land cover in the context of spatial planning problems. The research was conducted on valley areas protected under the Natura 2000 programme and that are located within the zone of influence of a big city. The researchers analysed local planning documents to see whether they were in agreement with the aims of the protection programme. The Natura 2000 areas located in the Commune of Stęszew, Poznań County were chosen for a case study. The article describes recurrent problems and phenomena that are typical of the protected areas and that are simultaneously affected by the pressure of urbanisation. GIS tools were used to make a comparative analysis of six categories of land use forms in three research periods and to calculate the indicator of land cover variance. Since the 1980s, the areas under study have been affected by changes in land use. They have been manifested by a higher forestation rate, increasing numbers of developed areas, and a decrease in farmland area. The percentage of other components of the land cover structure has not changed much. In view of environmental protection, the changes proposed in spatial plans are a matter of special concern. The territory under analysis is characterised by a very high land cover variance indicator referring to the developed area, whereas the indicators referring to farmland and wetland areas are negative. It is particularly difficult to apply the rule of sustainable development in the areas. The protection of natural values and the developmental needs of the commune stand in opposition to each other and cause spatial planning conflicts.