This study provides pioneering research on the vegetation of archaeological areas in Iran to enhance its naturalistic and bioindication values by selecting the Pasargadae World Heritage Site (WHS). Vegetation surveys were carried out in different homogeneous habitats, analyzing the plant communities through statistical elaboration, syntaxonomic role, mapping, and enhancement of plants with conservation interest. In an ecological approach, the study included an analysis of the recent climate changes and human interventions influencing the water resources. Results revealed seven main vegetation types reflecting ecological gradients shaped by environmental, edaphic, and anthropogenic factors. The syntaxonomic analysis showed a primary subdivision in semi-natural grasslands and synanthropic vegetation. Several key species were identified as bioindicators of multiple factors, such as: Launaea acanthodes, Stipa barbata, Alhagi maurorum, Bellevalia saviczii, Glycyrrhiza glabra, Convolvulus arvensis, and Hordeum murinum. The vegetation map showed how the hilly grassland communities hosted the highest number of species with conservation interest and their need to be better protected. Bio-climatic data, such as the construction of dams and the exploitation for irrigation purposes, pointed to the increasing xeric conditions, which make urging conservation efforts for the site’s historical and naturalistic values. The study underscores the importance of preserving places with high plant diversity for effective site management, and enhances the intricate relationship between vegetation and natural features in the occurring environmental changes.