The main aspects of systems efficiency are considered. It is shown that evaluating the efficiency of the functioning of systems can be both a single-criterion and a multi-criterion task depending on the objectives of the study. The correct statement of the problem of evaluating the effectiveness as an integral character in the general case allows only a multicriteria interpretation since in this case a combination of various factors affecting the system is taken into account. Information is provided on existing approaches to assessing the effectiveness of systems that use a large number of criteria for evaluating, which differ in their functional composition. A methodology for multicriteria functional efficiency assessment is proposed, which allows modeling the multifactorial dependence of performance indicators based on integral indicators expressed as radius vectors in multidimensional subject space, and forming a spectrum of various managerial actions and decisions based on the results obtained. The application of the presented assessment model for determining the options for navigation complex with the best and worst implementation for a set of technical parameters is shown.