Large cities face growing challenges of waste disposal due to the increase in urban population, economic development, and goods consumption, resulting in congestion, noise, and air pollution. The traditional trucking of waste material from collection points to landfills or garbage incinerators is no longer viable due to shrinking landfill capacity, stringent environmental regulations, and scarcity of land in urban areas. Recognizing all of these, New York City (NYC) initiated the first marine highway request for proposals (RFP) in the USA calling for a new waterborne proposal to export its residential waste material out of the region. An energy-from-waste (EFW) leading firm, seizing the opportunity, contracted us to develop an intermodal system. We developed a multimodal transportation system for the EFW firm and NYC that could eventually become a model and a solution to the mounting problems of urban waste management around the world for cities on the waterfront. Our approach consists in shipping the waste material to a power plant out of the city that generates energy from waste, with guarantees of state-of-the-art pollution control technologies. This poses transport challenges. We used a supply chain approach to illustrate the viability of a large-scale container intermodal system (truck–water–rail) via waterways and marine terminal facilities. This approach is built on containerized equipment, watertight container compartments, and intramodality. We used statistical analysis of daily waste volumes applied to standard weekly waste amounts and holiday peaks to determine the demand for tugs, barges, railcars, and containers, including a degree of redundancy. This paper presents the analysis results, from modeling and simulating to the system implementation that was used by the EFW firm to become the first waste disposal waterborne operating system in NYC and a model to emulate elsewhere. The operation, now fully implemented, reduces the number of truck miles driven, wear-and-tear on the roads and trucks, fuel consumption, congestion, noise, and pollution. The paper demonstrates that intermodal solutions are viable for large-scale waste disposal in major urban areas, utilizing existing waterways. A marine highway system is critical to solve goods movement problems and the growing challenges for urban freight movement and waste disposal.