The degradation of natural ecosystems triggers global environmental, economic, and social problems. To prevent this, it is necessary to identify the aptitude of priority areas for conservation or use by considering land fragility from multiple environmental and spatial perspectives. We applied the concept of environmental fragility to a hydrographic basin in southeastern Brazil that establishes (i) potential fragility levels according to slope, soil classes, geological domains, drainage hierarchy, and rainfall information using an algebraic map, and (ii) emerging fragility levels via the addition of the land-use parameters. The methodological approach involved the integration of the analytic hierarchy process (AHP) and weighted linear combination (WLC) into a geographic information system (GIS). The medium and slightly low fragility classes predominated in terms of potential (~60%), and emerging (~70%) environmental fragility models used to model the basin. The model indicated that high and extremely high potential fragilities were concentrated in the upper basin, a region that is considered a global biodiversity hotspot. The areas with high/extremely high classes of emerging fragility in the upper basin decreased, indicating that the natural cover classes and land-use types are not in danger. We also introduce acceptable conservation practices for land management and use according to the environmental fragility categories established in the present work. The methodology applied in this study can be replicated in other global ecoregions. It provides low-cost territorial and environmental zoning and flexible replication and can be adjusted by administrators who are interested in land-use planning.