The rapid economic expansion has catalyzed urbanization within urban agglomerations, thereby increasing flood risks due to changes in surface characteristics and atmospheric boundary layer properties. This research takes the Fujian Delta urban agglomeration as an example to explore the connections between flood risk and gross domestic product (GDP) growth across 29 districts during the period from 2010 to 2020. Our analysis reveals that flood risk distribution is spatially clustered at the scale of urban agglomerations, with clustering patterns strongly associated with levels of urbanization and economic development. Specifically, in highly urbanized districts, high-risk zones are dispersed throughout the urban areas. In contrast, in moderately to highly urbanized districts, although high risks are randomly distributed within urban areas, there are significant ‘high-high’ risk clusters at the urban edges. In less urbanized districts, these high-risk clusters predominantly occur within the urban centers. Drawing on these spatial correlations, the study proposes adaptive flood risk management strategies that consider the diverse urbanization and economic statuses within the agglomeration. This research not only sheds light on the intricate dynamics between urbanization, economic growth, and flood risks but also lays the foundation for future studies aimed at incorporating more extensive socio-economic factors to bolster urban resilience against climate-induced hazards.