Estimating the ecotourism carrying capacity (ETCC) in protected areas (PAs) is essential for minimizing the negative impacts of ecotourism and sustainable environmental management. PAs are one of the prominent ecotourism locations and many of these areas have been created to protect biodiversity and improve human wellbeing. This study has identified and prioritized negative impacts of ecotourism in Lar national park, the Jajrud protected area with the sustainable use of natural resources, and Tangeh Vashi national natural monument. For this purpose, physical carrying capacity (PCC), real carrying capacity (RCC), and effective carrying capacity (ECC) were estimated using the ETCC model. The results indicated that due to these areas’ ecological sensitivity, the most negative impacts of ecotourism are related to the environmental-physical dimensions. In contrast, the lowest impacts have been observed in the economic-institutional dimensions. Moreover, the results revealed that the highest PCC is related to Lar national park, and the lowest PCC is associated with Tangeh Vashi natural monument. There are more tourists in the Jajrud protected area with the sustainable use of natural resources than other areas in RCC and ECC due to low levels of restrictions and legal instructions. In contrast, in Lar national park and Tangeh Vashi natural monument, due to the short duration of ecotourism in these areas (from June to October), high level of restrictions, and ecological sensitivity, the number of tourists is less than the RCC and ECC. As these areas have a limited ability to attract visitors and ecotourism, the protection of these areas requires the implementation of sustainable management to control the negative impacts of ecotourism and estimate the number of visitors.