The increasing interest, and the actual necessity, for adequate means to evaluate how sustainable human activities are, has led to efforts to define indicators of sustainability. We propose the use of ecological indicators of sustainability that take into account the hierarchical structure of biodiversity, distinguishing composition, structure and function at the different levels of biological organization: ecosystem and landscape, community, and population and genetic levels. We evaluated the advantages of selecting and combining indicators of different hierarchical levels by examining several use and management projects. Examples of transformed land like large-scale plantations, perform well when evaluated by ecosystem-level indicators, but lead to neglect of some composition and structure components if evaluated at different levels. Limitations in using a small number of indicators become evident in cases of intensive exploitation of resources, such as the extractive reserves, which yield good results under the ecosystem and community levels, but fail under the population and genetic indicators. Wild species management, a common example of the use of population-level indicators, do not perform well under other indicators at broader scales. We also reviewed projects that are sustainable at different hierarchical levels, like some multispecific exploitation forestry management, in which harvesting of resources is at or below sustainable levels, selective extraction is performed, and where natural regeneration and recruitment of species is allowed. It is evident that the adequacy of indicators is not universal and must take into account the complexity of processes and variables involved in the different biological levels and human components, highlighting possible conflicts and contradictions, while increasing knowledge about maintenance of quality in the use and exploitation of resources that the relevant stake-holders regard as important.