Meighan watershed habitats, located in central Iran (Markazi Province), have undergone considerable changes in recent years. Landsat satellite images of the year 2020 were used to produce digital land use maps for the present study. Ecological quality, rarity and risk assessment analyses were performed using the Sub-Watershed-scale Ecosystem Service Modeler according to the InVEST (SWESMI) toolkit, HQR and HRA models. The images were classified into three classes including Agriculture, Rangeland, and Human-made (industrial-residential regions) impacts. The results indicated that there are three important habitats in the Meighan watershed: mountains, plains, and wetlands. Human-made changes, agriculture, and road developments were among the biggest threats and most devastating stressors in the Meighan watershed. There was an increased cumulative risk in the plain habitat of the Kharahrod (31.44%), Amanabad (27.75%) and Sarogh (26.87%) sub-watersheds. A decreased cumulative risk was identified in the mountain habitat of the Kheirabad (7.62%) sub-watershed in the Haftad-Gholleh National Park, and wetland habitat of the Meighan (4.30%) sub-watersheds. The plain habitat (with high cumulative consequence) and the wetland habitat (with high accumulative exposure) are at the highest risk from Human-made activities. Stressors related to roads and agriculture-livestock were the main stressors in the mountain habitat and wetland habitat, respectively, whereas both stressors were considerably high in the plain habitat. Due to being located in a protected area, the Kheirabad sub-watershed was found to have suitable quality and rarity compared to other sub-watersheds in central Iran. The results highlight the significance of land conservation and protected areas in maintaining the habitat quality and reducing the risks associated with habitat degradation and biodiversity.