This study was carried out to evaluate the use of inland transportation and its effect on logistics system in Nigeria using Lagos State Waterways Authority. To achieve this objective, four research questions and three research hypotheses were formulated to guide the study. The data was collected from both primary and secondary sources. The primary data were collected with the help of a well-structured questionnaire of two sections administered to staff and management of Lagos State Waterways Authority. The collected data were analyzed with tables and simple percentages to analyze the research questions while Chi-square statistical tool was used to test research hypotheses. The study reveals that there is a significant relationship between the effect of transportation and logistics systems in Nigeria. The study concluded with some recommendations that government should encourage the establishment of inland waterways companies to participate in a specialized shipping venture and to combine their operations with coastal shipping within West Africa and governments at various levels should involve in the formulation and implementation of policies and measures that will effectively promote enhanced accessibility through increased development of road networks.