Local air pollution is the most relevant externality of maritime transport, and its effects are more acute in urban areas as a result of manoeuvring, hotelling and load/unload activities at ports. This article is intended to assess ships’ local air pollution impact in generally densely populated harbour areas to decide whether alternative power supply measures are feasible. First, an optimized infrastructure investment model is developed to ease implementation and maximize the efficiency of alternative power supply projects. Once target harbours and traffic (ship types) within a national port network have been chosen, a vessel traffic analysis (ship type, tonnage, manoeuvring, and hotelling times) is carried out to quantify and evaluate annual polluting emissions (PM2,5, SO2, NOx, and VOCs) and their externalities. Finally, the assessment model is applied and results of the Spanish port network case study are discussed. The results obtained are significant and bring the possibility of further controlling the ship’s environmental performance at berth.