With the increasing frequency of extreme weather events driven by climate change, Nature-based Solutions (NbS) have attracted growing global attention; however, their engineering framework remains underdeveloped. This study defines river basin flood control as a two-tiered system—density management and energy management—and proposes an operational framework based on this structure. As an index for the first tier, density management, we introduce the spatio-temporal effective rainwater density \(\:{\rho\:}_{ster}={V}_{e}/(A\cdot\:{T}_{fd})\), where \(\:{V}_{e}\) is the total volume of effective rainfall, \(\:A\) is the catchment area, and \(\:{T}_{fd}\) is the flood duration. Reducing \(\:{\rho\:}_{ster}\:\)can be pursued by decreasing \(\:{V}_{e}\) or extending \(\:{T}_{fd\:}\)offering an interpretation of the “slowing the flow” concept advocated in NbS. The second tier, inundation flow control, addresses the management of kinetic energy and momentum of floodwater once inundation occurs. Based on these two tiers and three phases—conservation of soil structure, control of water mass and state, and control of flow energy and vector—ten technical elements for river basin flood control were identified and organized. Each element was drawn from physical laws, historical flood control practices, and the authors’ engineering experience. Water balance analyses of two Japanese flood events were compared using depth-equivalent values (mm). In the predominantly non-urban Kuma River basin, approximately 50% of total rainfall was retained as basin storage, whereas in the urbanized Zenpukuji River basin, approximately 18% was retained. In both basins, basin storage continued to increase until the cessation of rainfall, even under extreme precipitation. This result suggests that the functions of technical elements contributing to density management may not be entirely lost during heavy rainfall events. As flooding cannot be entirely prevented under climate change, inundation flow control technologies become increasingly important, and their effective implementation calls for co-creation with local communities.