This article is based on the observation that the affected populations perceive existing community‐based adaptation strategies to the health effects of floods differently. We explore the resilience of the local health system to climate change (CC) in Keur Massar (Senegal) using a monographic approach based on a qualitative survey of flooded households, health professionals, hygiene agents, community health actors, administrative and local authorities, agents from the Ministries of Health and Environment, and experts from the ecological and meteorological monitoring centre (n = 72). The effects of CC on health are modulated by financial, organisational, social and cultural factors. The effects of CC on health are modulated by traditionally praised by self‐centred health governance, which is often based on standardisation of problems and thus not sufficiently attuned to local contexts, especially the climate vulnerability index (CVI) of households and health structures. Despite the existence of programs to combat the consequences of CC, the notorious lack of exhaustive mapping of areas with a high CVI hinders the effective management of the health of the affected populations. A typology of forms of mobility in the context of flooding—ground floor to the upper floor, borrowing a room, renting a flat, seasonal residence—reveals inequalities in access to care as well as specific health needs management of vector‐borne diseases, discontinuity of maternal, newborn and child health care, and psychosocial assistance. The article outlines how a health territorialisation based on surveillance and response mechanisms can be co‐constructed and made sustainable in areas with a high CVI. Integrating this approach into national health policies allows for equity in health systems efficiently and sustainably.