Morphodynamic changes in the riverbed may be accelerated by the climate change-induced effects, mostly through the increase of the frequency of extreme climatic events such as floods. This can lead to scouring of the riverbed around the bridge substructure and consequently reduces its overall stability. In order to better understand hydromorphological processes at the local scale, the influence of floods on bridge scour requires a detailed analysis of several interacting flood hydrograph characteristics. This paper presents a multivariate analysis of the annual maximum (AM) flood discharge data at four gauging stations on the Drava and Sava Rivers in Croatia (Europe). As part of the hydrograph analysis, multiple baseflow separation methods were tested. Flood volumes and durations were derived after extracting the baseflow from measured discharge data. Suitable marginal distribution functions were fitted to the peak discharge (Q), flood volume (V) and duration (D) data. Bivariate copula analyses were conducted for the next pairs: peak discharge and volume (Q– V), hydrograph volume and duration (V–D) and peak discharge and hydrograph duration (Q–D). The results of the bivariate copula analyses were used to derive joint return periods for different flood variable combinations, which may serve as a preliminary analysis for the pilot bridges of the R3PEAT project where the aim is to investigate the influences on the riverbed erosion around bridges with installed scour countermeasures. Hence, a design hydrograph was derived that could be used as input data in the hydraulic model for the investigation of the bridge scour dynamics within the project and a preliminary methodology is proposed to be applied. The results indicate that bivariate frequency analysis can be very sensitive to the selected baseflow separation methodology. Therefore, future studies should test multiple baseflow separation methods and visually inspect the performance.