The problem of understand natural processes as factors that restrict, limit or even jeopardize the interests of human society is currently of great concern. The natural transformation of flood waves is increasingly affected and disturbed by artificial interventions in river basins. The Danube River basin is an area of high economic and water management importance. Channel training can result in changes in the transformation of flood waves and different hydrographic shapes of flood waves compared with the past. The estimation and evolution of the transformation of historical flood waves under recent river conditions is only possible by model simulations. For this purpose a nonlinear reservoir cascade model was constructed. The NLN-Danube nonlinear reservoir river model was used to simulate the transformation of flood waves in four sections of the Danube River from Kienstock (Austria) to Štúrovo (Slovakia) under relatively recent river reach conditions. The model was individually calibrated for two extreme events in August 2002 and June 2013. Some floods that occurred on the Danube during the period of 1991-2002 were used for the validation of the model. The model was used to identify changes in the transformational properties of the Danube channel in the selected river reach for some historical summer floods (1899, 1954 1965 and 1975). Finally, a simulation of flood wave propagation of the most destructive Danube flood of the last millennium (August 1501) is discussed.