Nowadays great attention is being paid to the ecological aspects of maritime transport functioning, including the problem of pollution and emission of poisonous substances from ships. Such emissions have a significant impact on the environment and sustainable operation of ports, especially those located close to intensive waterways. A decrease in emissions from ships may be achieved by implementing different methods, among others, through the use of environmentally friendly fuels, electrical and hybrid vehicles, as well as through the improvement of port approach and inside navigational channels, optimization of the transport processes organization, etc. However, the size of the influence of ships’ crew and ports pilots’ qualification on the possibility to decrease the emissions from ships during maneuvering in port areas remains a question. This article aims to develop a method to assess the possible decrease of the emissions from ships in ports, considering human factor influence. The method has been developed and verified on the selected case study example. The influence of ships’ crew and ports pilots’ qualification on time spent on maneuvering operations by ships in port areas and consequently the volume of emissions has been investigated. The research results show that for the set conditions it is possible to reduce emissions from ships up to 12.5%. For that reason, appropriate education and training are needed to improve the qualifications of decision-makers performing ship maneuvers at ports areas.