The analysis of the results of numerical hydrodynamic modeling of water level and current fluctuations of the Baltic Sea in the periods of floods in the Finland and Riga gulfs is carried out. It is shown that due to the considerable isolation of the sea a great influence on the dynamics of flood waves have the processes they reflect, resulting in a generated progressive-standing waves. During a especially dangerous sea level rise on January 9, 2005, the flood wave had a period of about 40-42 hours. This period turned out to be close to the 41-hour period of the Baltic Sea, distinguished on the basis of an analysis of the results of numerical hydrodynamic modeling of free Baltic Sea level oscillations. The spatial structure of the level field for eigenoscillations with a period of 41 hours allows them to be identified as multinodal progressive-standing waves, characterized by a large number of amphidromic systems and antinodes. One of the most pronounced antinodes of eigenoscillations with a period of 41 hours is in the Neva Bay of the Gulf of Finland.