Conservation of biodiversity in arid lands is a major issue worldwide. Knowledge of the biodiversity present is key to promote and facilitate the conservation of endangered native plants and will contribute to their persistence. The Atacama Desert, located in southern Peru and northern Chile, is considered a priority area for biodiversity conservation, principally due to high levels of endemism in the ecosystem. On this basis, water traits of plants are a useful tool for developing cause-and-effect relationships of abiotic variables under water stress environments. Nevertheless, currently there is lack of information about the influence of ecological factors on reproduction parameters, and the interaction among climatic variables and plant water relations that influence seed production in plants that inhabit water-limited environments. This report reviews the importance of incorporating plant physiology for the conservation of endangered vegetation as a predictive tool for management and preservation plans. Moreover, the report highlights the necessity of incorporating new protected areas, due the recent increase of species listed as endangered in the Atacama Desert. In brief, these two topics must be considered to promote the recovery of endangered biodiversity in hyperarid areas, taking into consideration soil erosion, climate change and industrialization processes.