The European Union (EU) ensures the conservation of biodiversity through the Natura 2000 Network, which establishes the classification and selection of protected areas at European level. Unfortunately, member countries cannot make the best zoning decisions for biodiversity conservation because there are no clear and uniform parameters to designate Natura 2000 sites. Due to this, it is convenient to evaluate the importance of the criteria for biodiversity conservation through a general assessment, which could establish relevant criteria that can be analysed through geostatistical methods combined in multicriteria analysis. This paper aims to consider biodiversity importance values taking into account land use, so that it is possible to develop a zoning proposal which verifies or corrects the suitability of the designated areas for the Natura 2000 Network in Castilla y León, Andalucía and Madrid (Spain). The choice of these regions allows us to compare areas with a high variability of population density, making possible to compare the potential protected areas with respect to the population living in each area. This assessment has been performed using basic and easily adaptable criteria of biodiversity conservation, so it could be applied in other European territories. In this way, clear and uniform parameters for zoning will be used, being possible to detect the best protected areas. One of the most important purposes of the Natura 2000 Network is to increase connectivity between territories; our work proposes new areas that could be linked to currently protected territories, to favour the achievement of this purpose of the Natura 2000 Network.