The author, a researcher at the Maritime Academy in Szczecin, has been conducting research in the field of waste management in ports of the European Union for many years. The purpose of this paper is to present the waste management system in the context of pollutants that remain in ports. The field of the research will include the ports of Szczecin and Świnoujście, which are in the close relationship with the other ports of the European Union. The results of the analysis for the years 2005–2009 were used to assess the current waste management system and can be used in practice to improve the used solutions. The system of collecting waste from ships, was represented by JSC Seaport Authority Szczecin – Świnoujście on February 1, 2004. Due to incomplete data in this study a transitional period – the year 2004 was not included. It should be emphasized, that the data analysis has not previously been published. The study was based on the latest requirements of the European Union