The Neva Bay is a body of water located between the delta of the Neva River and Kotlin Island. The goal of the study was to develop a method for numerical modeling of the shallow water equation in the Neva Bay, based on the finite element method. To achieve this goal, we solved a number of tasks. First, we selected characteristic periods in the history of the Neva Bay and formed numerical modeling options while determining boundary conditions. Secondly, we determined the geometric characteristics of the computational domain for modeling options and formed a finite element mesh for each of the options. Then, we found a numerical solution of hydrodynamic problems in terms of determining values of current velocity vectors. Finally, we conducted a comparative analysis of the results of solving the hydrodynamic problem of the structure of currents in the Neva Bay in different periods of history. The changes in the velocity field occurred because of the construction of the fairway and the dams for the Complex of flood protection structures (CFPS) in St. Petersburg. Today there is practically no water flow south of the Sea Canal. Water exchange between the Neva Bay and the Gulf of Finland is carried out due to culvert structures in the northern part of the CFPS and navigation facilities. The average flow of the Neva River during the calculation period did not change and was about 2500 m3/s (depends on the water level in Lake Ladoga); an increase in speeds occurs north of the Sea Canal.