This work aimed to study the structure of bacterial film grown on the inner tuber surface of the flow reactor. Applying scanning electron microscopy (SEM) approaches, the detailed biofilm relief was visualized. The action of electrochemically aqueous solution on the fine structure of biofilms generated by plankton forms of lacto bacteria and E.coli was investigated. Electrochemically aqueous solution treatments were able to destroy the biofilm organic polymer matrix and bacterial cells embedded in a matrix. It is shown that the working of a bacterial film with alkaline catholyte destroys the main components of the biofilm, has a significant purifying and disinfecting effect. One of the criteria for the effectiveness of biofilm purification is the morphological analysis of the presence of fragments of the matrix or cellular component on the specimen surface. By the SEM method, the presence of a residual organic mass on the surface of the substrate after treatment was observed. This is a factor that can provoke de novo formation of a population of microorganisms on the surface of the pipeline surface. Thus, the most important task of cleaning and disinfection of the pipeline is the removal of microbial cells and residual fragments of the biomatrix.