The motion of humans and commodities from one scene to another using various vehicles and facilities is known as transit. It's also critical to economic growth and people's health because it allows them to work, go to school, make purchases for food and other necessities, and participate in all of the activities that contribute to human life. Using the waterways transportation system has the benefits of reducing road traffic congestion, provides a significant source of income to the public treasury, brings multiple employment options for employees, minimal operational costs, free natural transport network, marking development to towns through the connection with canals, air pollution and savings cost. In this study, we present a goal programming (GP) model to optimize waterway transportation in a location with road congestion to enhance the transportation system. The goal programming approach is applied from the data of the Lagos State Waterways Authority (LASWA) in Nigeria. The goal programming method is effective and the findings indicate the potential to increase the number of commuters using the waterway transportation from 7,640 to 10,026. Also indicated in the findings were the reduction of fares as potential cost reductions by ₦200.00, reduce travel time by 4 minutes, and increased vessel numbers of Ebute Ero -Ikorodu ( 2x ) to 528/540. The findings and approach are generalized for waterway transportation optimization.