The existing methods to study the movement and pattern of flow in wells with electric submersible pump (ESP) within the ‘bottomhole-pump-wellhead’ system are rather experimental and empirical. Hence, the lack of universal techniques considering all possible operating modes of wells does not allow using the existing techniques to elaborate the measures improving the efficiency of well operation with ESP. Besides, these techniques cannot always be applied to define the optimum operating modes and to determine the need for various well intervention jobs as they are not quite perfect. The improvement of profitability of well operation is intimately connected with deliberate change of flow properties and structure considering various physical properties of fluids and ESP-based operating modes with further formation of fine emulsions. In this regard, the modern petroleum industry is facing an urgent task to study the processes in a bottomhole and a wellbore zones using a generalized mathematical model with further analysis of various perturbing actions on emulsion stability, assessment of its decrease and separation of the water phase within subsurface equipment.