Rural areas are highly vulnerable to floods due to limited social, economic, and physical resources. Understanding rural vulnerability is vital for developing effective disaster risk reduction strategies. Even though rural areas and cities are intrinsically linked, rural vulnerability was assessed without considering its relation to cities. Numerous theoretical frameworks on systemizing and assessing vulnerability were developed with varying level of scope and depth in terms of scale, dimensions, and components. Nevertheless, these frameworks did not explicitly mention the impact of flood or other hazards on the linkages between spatial units i.e., rural and urban. This study aims to understand and conceptualize the rural vulnerability with respect to the dynamics of rural–urban linkages in the case of flood events. To do so, current literature on rural–urban linkages, vulnerability, as well as factors that influence them were critically reviewed. Taking into account the main elements of rural–urban linkages (flow of people, information, finances, goods and services), components of vulnerability (exposure, susceptibility, and capacity), and factors (social, economic, institutional, infrastructural, spatial, and environmental), a unified framework is proposed. The framework underscores that the role of rural–urban linkages is essential to fully understand rural flood vulnerability. Moreover, the framework highlights the role of spatial factors—city size and proximity to the city—as crucial to comprehend rural vulnerability. This framework can be used as a tool for understanding multifaceted rural vulnerability for climate change adaptation and disaster risk reduction considering spatial development perspective. In this context, empirical investigations can be made to validate the proposed framework and policies can be introduced accordingly. Overall, the proposed framework can help recognize concepts and links of vulnerability, rural–urban dependencies, and rural development dynamics.