The article describes the work of the seaport transport-technological system (TTS). Spend controlling analysis of the basic processes and port operations. It was found that the construction of an optimal system of controlling processes, leading to increased efficiency of the port. We consider a variety of factors that affect the efficiency of the port of reloading works and the importance of quality of work at every stage of the process. In order to determine the level of the expected impact of controlling the use of the analysis of the construction of the port of the quality management system, which is taken as a basis for the organization of transport and technological system of the port as a whole. It determined that the efficiency depends on the turnover of the port and thus the quality and quantity of treated vessels. At the same time your system needs to build their own port, to meet the requirements of customers, and dependence of the amount processed by the courts from time to time is the reciprocal of. The authors propose a model of controlling the transport and port system technology, taking into account factors that affect the process efficiency. The scheme of internal communication processes, transport and port systems technology, as well as take into account the external communication with customers. Use of risk systems in the port processes allows us to consider its bottlenecks, and provide impact of pointing it to a particular element of the system, when it is needed, that is applicable to many processes, owls, and is a universal method to increase the efficiency of the enterprise.