The problems of modeling the operation of classic (constant configuration) and variable vessel combination of barges by matrix routing methods are discussed in the paper. Regrouping the combination directly on the route allows you to operate a larger number of barges compared to a permanent combination, which increases its load capacity. The efficiency of water transport is determined by the volume of cargo delivered in relation to operating costs, which depend on the time the vessel is on the route. Additional stops during the voyage of the vessels combination for its reformation allow to increase the total cargo turnover, but lead to an increase in the voyage time, which is a certain contradiction, the solution of which is possible through the use of a variable approach to organizing the work of barge-tug combinations. The results of the mathematical apparatus development for describing the model of the barge-tug combinations movement on inland waterways are presented; the influence of turns on the change in the combinations speed and on the total voyage time is taken into account, and a particular task of regrouping the combination is additionally considered. The route from the Nizhnesvirsky lock to Ladoga Lake, on which turning points and places, where it is necessary to change the barge-tug combinations configuration to pass it are identified, is analyzed. For the mathematical description of the vessel movement along the route, a system of calculation matrices, which allows us to generalize the change and relationship of the speed and time parameters of the vessel movement with its route, including taking into account the time of regrouping the combination, is proposed. The main factors influencing the effectiveness of the combinations operation organization with their reorganization along the route are identified. As a basis for constructing matrices, it is proposed to use turning points, the system of which is formed in the form of a three-level model. The complex of matrices allows to obtain a quantitative presentation of the vessel movement and voyage time, while providing detailed parameters for the combination passage along the individual sections of the waterway, which in general is the basis of the developed information technology for intelligent control of the barge-tug combinations operation.