The aim of the research is to identify and quantify the direct economic effects resulting from the improved seaport nautical access and capacity expansion. This case study considers a regional port located in the Baltic sea and relates to port users, i.e., shipping operators and shippers. The effects were identified for maritime transport by comparing transport performance in two scenarios: with-the-investment and without-the-investment. Incremental calculus addresses freights (containers, dry bulk, and cereals) traded to and from the given port, changes in size of vessels, and the shipping route alternatives vis-a-vis adjacent ports in the range. Sustainable impact concerns generalized maritime transport cost, i.e., shipping operating costs and port-to-port transit time, as well as energy consumption and external costs of maritime shipping. To capture effects, daily and unit dry bulk, as well as container shipping cost, values of time, and marginal external costs were revealed in freight sea transport. As investigated, shipping operators and shippers will benefit from the reduction in ships’ operating (including ships’ fuel cost savings) and time cost, while the community will enjoy the reduction in externalities. However, the main economic effect is the reduction in shipping operating cost resulting from the increased vessel size (economies of scale).