Important attributes of a transportation chain are the costs of their operation, the security of supply they provide, and reducing carbon emissions throughout the chain. When making managerial decisions about the chain configuration, shippers consider the optimal choice of means of transport, carriers, or ports. Seaports, as transport nodes, determine the functioning of supply chains they serve. A constant process observed in the world shipping is the consistent increase in the average size of ships. Adapting the port and port access infrastructure to the changes observed in the world shipping is a prerequisite for maintaining the competitive position of the port, and consequently of the entire transport chain. Adequate hydrological conditions ensuring safe access to ports for increasingly larger ships are necessary for the stable functioning and development of a port and the entire region. For shippers, the certainty that the handling of larger vessels is assured regardless of any fluctuating hydro-meteorological conditions and temporary vessel entry permits is a guarantee of security of supply. This study aims to demonstrate the impact of fairway deepening on port-oriented supply chain costs and security of supply, as well as verification of the importance of these factors for cargo shippers’ decision-making. The article used the case study method based on the port of Szczecin, for which the investment of deepening the fairway to 12.5 m is being implemented. The article estimates the transport costs of five transport chains served by the port of Szczecin. Our research showed that a 2.5 m increase in the permissible draught of ships results in a decrease of up to 25% in transport costs resulting mainly from the reduction in specific fuel consumption throughout the chain. The analysis of the results showed that a secondary benefit of deepening the fairway can change the structure of the port’s foreland. This conclusion was validated by means of in-depth interviews held with selected shippers cooperating with the port of Szczecin. An additional outcome of the interviews was identification of the remaining conditions that should be met to take full advantage of improved port accessibility. The research is the first step to broader studies assessing whether improving quality of port infrastructure can contribute to a reduction in emissions from ships in a port and thus facilitate the transition to zero-emission ports.