Lakes are typical plain reservoirs, with many similar functions to valley reservoirs; however, their flood processes differ significantly due to their specific topography. Flooding of the dam site, the entire reservoir inflow, is considered during flood control analysis of valley reservoirs. Whereas, the flood inundation risk of flood detention areas in the lake basin should be considered for lakes. Therefore, more attention should be paid to the flood processes of each sub-region. Here, based on the flood processes characteristics of large water-carrying lakes, a complete framework for establishing design floods for sizeable rivers-connected lakes is introduced. First, multiple Copula-based joint distribution functions are constructed based on the water system structure of the lake. Then, several confidence intervals are obtained using a methodology that identifies the boundary for multivariate combinations. Finally, through these confidence intervals are used in conjunction with each other, the design flood processes for water-carrying lake system can be determined. The proposed methodology was applied to the Hongze Lake, China. The results indicate that this method not only effectively avoids the randomness of the traditional method but also balances the characteristics of the flood process in each sub-region with the features of the entire flood process. The proposed method has a strong statistical theoretical foundation and expands the applicability of multi-variable flood frequency analysis techniques to water conservancy projects.