Abstract Background Climate change represents the paramount challenge to global health, disproportionately impacting particular vulnerable individuals and communities. By identifying and elucidating disparities in health-related climate risks among these groups, we can facilitate the development of appropriate and equitable climate adaptation strategies. This research identified climate-related risks, health perceptions and needs, and behaviors among Jewish and Bedouin populations in the Negev Desert, a region highly susceptible to climate change, located at the intersection of geographical and social marginality. Methods Ten focus groups (n = 69) among vulnerable Jewish and Bedouin residents were conducted and systematically analyzed to identify disparities in health-related climate risks and behaviors. Vulnerabilities were defined based on income, age, health status, living environment, and outdoor activities. Results The findings highlight both shared and distinct difficulties and barriers vulnerable Jewish and Bedouin Negev residents face in the context of climate-related health risks. Key themes that emerged address: a) the direct and indirect impacts of climate-related events on health and well-being; b) the exacerbation of climate-related health risks by existing vulnerabilities and systemic barriers; c) the pivotal role of community resources in coping strategies; and d) lack of trust in the state and its institutions which underpin climate-related experiences. Conclusions The complexity of coping with climate change encompasses individual, community, and national/institutional levels. Vulnerable populations’ experiences with climate change are impacted by factors such as poverty, social marginality, violence, and barriers to accessing healthcare and other services, and is not a standalone phenomenon. Therefore, climate change adaptation and mitigation cannot be distinguished from other challenges impacting the health and well-being of populations. Key messages • Climate adaptation efforts must integrate with broader social and health strategies to effectively support vulnerable groups. • Community resources and trust in institutions are crucial for vulnerable populations facing climate change impacts.