Water transport being among the oldest mode of transport is crucial to the development of any nation. It provides means of transportation for both rural and urban dwellers, particularly along the coastal areas and inland waterways. It is a known fact that water transportation has been neglected for a long period by both the government and the private sector, particularly in the area of safety of passengers on Lagos waters. This paper examines the perception of safety and the use of water transportation among passengers within Lagos metropolis. The jetties were purposively determined. Using a random sampling technique, a structured questionnaire focusing on socio-economic characteristics of passengers, use of water transport, reasons for the use of water transport, perception on safety and frequency of water transportation usage were administered to 1050 passengers across the selected four jetties (Liverpool, Falomo, Bayeku, and Ijegun Egba) within the metropolis with a response rate of 86.3%. The step-wise multiple regression results show that passengers’ perception of poor safety of water transportation predicted a significant 78.1% of reluctance to travel by water within Lagos metropolis (F = 27990.685, p<0.05). This study, therefore, recommends that the state government should provide adequate safety measures that could repose confidence in passengers in order to increase patronage of water transportation. This singular act could help to reduce the incessant traffic congestions on Lagos roads.