Assessments of the conservation status of natural resources have been conducted at large (i.e., global, continental, and countrywide) extents. Studies at finer scales, however, can yield increased detail needed to identify conservation strategies for smaller scales which can contribute to goals at the larger extents. Our study was conducted at the scale of a single state, San Luis Potosí, in Central Mexico. Although the state harbors great biological diversity, large areas covered by natural vegetation communities have been and continue to be destroyed by land use changes, cattle grazing, and mine-generated pollution. Our purposes were to quantify the proportion of distribution within natural protected areas (NPAs) of land cover classes, soil types, ecoregions, and altitudinal steps. In addition, within individual NPAs, we aimed at assessing risks. We conducted our analysis at the 1:1, 1:250,000, and 1:1,000,000 scales depending on layer availability. Our results show that actions within the state could contribute to federal and global conservation goals by protecting sites of globally imperiled ecosystems (cloud forests and natural grasslands). At a finer scale, we identified that piedmont scrubland, medium and low tropical moist forests, wetlands, and low elevation habitats are rare and/or constitute conservation omissions within the state. Similarly, ecoregions with mesquite, semi-deciduous, and moist tropical thorn forest, wetlands, and low elevations (<1200 m.a.s.l.) are conservation omissions or gaps. Finally, at the smallest scale, risks within some protected areas (PAs) include the presence of agriculture, cattle grazing, and mine tailings from mines dedicated to extraction of Au, Ag, Cu, Pb, and Zn. Therefore, management within these PAs should minimize such risks through identification of the most important conservation zones within the PAs, and implementation of local legislation prohibiting such activities at the immediacies of conservation zones. Approaches like ours within similar administrative units will help identify ecosystems that are vulnerable and not well protected. However, to prioritize conservation action it is also important to consider surrogates such as species from different groups and ecosystems, as well as rarity and complementarity of such surrogates.