Lagos State is endowed with international commerce, industry and infrastructure excellence drives. In Lagos State, traffic situation is chaotic and socio-economically unfriendly due to ills in multi-transportation modal functions. Urgent research and development attention is required to arrest total collapse of the entire modal system. In this study, a framework is developed for efficient utilization of Lagos waterway system as a complement to other transportation modes such as the dominating road mode. The paper has used passengers travel distances, travel times, travel delays and speed variations on road and water transportation systems in Lagos State to design a geographic information system (GIS) of waterway transportation system. This attempt has formed its base on graph theory, spatial interaction and urban transit capacity. The study has also designed a vector-based GIS for four (4) different spatial locations of the water transportation route network. Consequently, the water transportation at a peak hour commuter service that would complement existing bus, car and taxi in order to reduce the demand for road transportation in Lagos Metropolis was examined. From the study, water transport is found to have caused a reduced journey time by an average of 46.33%. Key words: Traffic, graph theory, passenger travel distances, travel times, waterways.