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This study analyzes the effects of climate variability and external shocks on the operational and economic sustainability of ethnotourism in the Emberá communities of the Upper Chagres. Since the 1970s, communities such as Emberá Drúa and Puru Biakiru have developed a socioeconomic model based on community management of natural resources and the preservation of their intangible cultural heritage, where the Chagres River and Lake Alajuela serve as the main means of connectivity and the core of their productive activities. Methodologically, a mixed-methods approach was employed, combining quantitative analysis of precipitation data with a qualitative case study based on fieldwork. The results show that the stability of this model has been affected by a dual crisis: the disruption caused by the COVID-19 pandemic in 2020 and the intensification of climate variability between 2023 and 2024. In particular, El Niño-related events led to extreme hydrological conditions that significantly altered navigation levels. The findings reveal a direct correlation between water deficits and the viability of community-based tourism. Reduced water levels critically impacted the use of traditional piraguas (dugout canoes), tripling travel times and increasing operational costs, with a 400% rise in fuel consumption. The study concludes that climate variability is a determining factor in the sustainability of ethnotourism in the Upper Chagres, highlighting the need to strengthen climate governance frameworks that incorporate the logistical, economic, and territorial needs of indigenous communities.