Wet underwater arc welding is now widely used. At the same time, obtaining high-quality welds with this welding method is an urgent scientific and technical problem due to their saturation with hydrogen and oxygen and the formation of pores. One of the promising directions for solving this issue is the use of an external electromagnetic effect on the liquid metal in the weld pool in order to control the movements of the molten metal flows to improve the degassing processes of welded joints. It is possible to estimate the parameters and efficiency of external electromagnetic influence by means of mathematical modeling of related electromagnetic, hydrodynamic and thermal processes occurring in the welding installation. The article proposes a three-dimensional integro-differential model of a non-stationary hydrodynamic process occurring in the liquid metal of a weld pool in an underwater arc welding system with an external electromagnetic effect. For the equations of hydrodynamics boundary value problems are formed, which, using potential theory, are reduced to a system of integro-differential equations for the vorticity function in the volume of a liquid conductor and a simple vector layer on its surface. For a numerical solution, the resulting system of integro-differential equations is approximated by an algebraic system according to the Krylov-Bogolyubov method. This system of equations makes it possible to determine the velocity field in the liquid metal of the weld pool for any welding modes.