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Abstract Studying the centennial or millennial timescale response of large rivers to changing patterns in precipitation, discharge, flood intensity and recurrence, and associated sediment erosion is critical for understanding long‐term fluvial geomorphic adjustment to climate. Long hydrographs, maintaining reliable Flow Duration Curves (FDCs), are a fundamental input for such simulations; however, recorded discharge series rarely span more than a few decades. The absence of robust methodologies for generating representative long‐term hydrographs, especially those incorporating coarse temporal resolution or lacking continuous simulations, is therefore a fundamental challenge for climate resilience. We present a novel approach for constructing multi‐century hydrographs that successfully conserve the statistical, especially frequency analysis, and stochastic characteristics of observed hydrographs. This approach integrates a powerful combination of a weather generator with a fine disaggregation technique and a continuous rainfall‐runoff transformation model. We tested our approach to generate a statistically representative 300‐year hydrograph on the Ninnescah River Basin in Kansas, using a satellite precipitation data set to address the considerable gaps in the available hourly observed data sets. This approach emphasizes the similarities of FDCs between the observed and generated hydrographs, exhibiting a reasonably acceptable range of average absolute deviation between 6% and 18%. We extended this methodology to create projected high‐resolution hydrographs based on a range of climate change scenarios. The projected outcomes present pronounced increases in the FDCs compared to the current condition, especially for more distant futures, which necessitates more efficient adaptation strategies. This approach represents a paradigm shift in long‐term hydrologic modeling.