The paper represents researches in the field of logistical processes in the context of interaction of various transport modes. The characteristics of forms of shipments' logistical organization in railroad and water communications were defined that differ from the existing ones by the performed functions and types of operators. This allows describing more precisely the organizational forms of interaction. The authors have developed an algorithm for managing operational activities in the logistics center, based on the interconnection of flows within it and coordination of the participant interaction in supply chains. The proposed methodological recommendations on the economic justification of the logistics center, which consist in the organizational support structure, allow providing a differentiated approach to the planning of operations for processing the flow according to the composition of the logistics chain.