Recent changes in climatic characteristics and consequent changes in the discharges and in the hydrological response of watersheds raise questions about the safety of water structures. Changes in flood wave characteristics (shape, volume, peak flow) may significantly affect the functionality of these structures. The study proposes a methodology for constructing design wave and flood hydrographs using discharge time series. A case study was carried out in the Little Carpathians watershed of the Parná River, above the profile of the Horné Orešany reservoir in Slovakia. The volumes and characteristic shapes of the flood waves with the maximum annual and seasonal discharges were determined using the Floodsep software. Subsequently, the T-year annual and seasonal discharges were estimated. Then, for pairs of the Tyear discharges and the associated volumes of flood waves, a joint probability distribution was constructed by copula functions. The associated volume of the T-year peak discharges was selected from the copula, and the probability of exceeding it was determined. Based on this analysis, a set of annual and seasonal control flood waves with the design maximum discharge, the associated volume with the selected probability, and the typical shape of the flood wave was constructed. This research provides satisfactory results for designing control waves necessary for assessing water structures with extreme loads and establishing a functional methodology for assessing other water structures in the region.