Decisions to invest in waterway terminals, where oil and oil products are moved and stored, should take into account aspects related to the logistics costs involved, as well as the existence of managerial flexibilities. The main objective of this work is to propose a methodology for the evaluation of investments for this type of unit with emphasis on future uncertainties and to evaluate a selected project in a Brazilian waterway terminal with the purpose of solving one of its main restrictions that ends up generating excessive costs of demurrage to the operation. The proposed step-by-step should be reflected in other analyzes of the oil and gas company, whose subsidiary operates the terminal in question. The economic evaluation of the project takes into account the modeling of uncertainties and the existing flexibilities, in the light of the Real Options Theory. The relevance of this work to the literature is the application of an evaluation of Real Options in a project of a Brazilian private waterway terminal, a scenario little explored by the authors of this area in the country, with emphasis on the occupation of its berths and the costs of demurrage. The contribution is made through the proposed framework for analysis of investments in terminals and the quantification of gains with the implementation of the evaluated project, which eliminates some current operational restrictions. In addition, the oil and gas company is expected to disclose the methodology internally and to formally adopt it in its Logistics investment assessments, including initiating a process of cultural change in the areas responsible for the projects and in the decision makers. The development of the study involves statistical data collection and analysis, interviews with terminal operators and company specialists, deepening of Real Options techniques, sensitivity analysis in the relevant variables and discussion with other collaborators interested in the subject. The results show that there is value in waiting for the investment, analyzed here in two scales.