The establishment of non-indigenous species in marine and freshwater environments is a worldwide issue and a concern to human and environmental health, and aquatic biodiversity. Oceanic shipping and transport has provided a global connection for species dispersal, which has greatly increased the potential for the rate of invasions. The main vectors for species introductions by ships are ballast water and sediments in ballast tanks. With existing technologies and recommended standards proposed by the International Maritime Organisation (IMO) we can partially control pollution. However, no method is efficient enough to remove all organisms from ballast water. Therefore, it was also proposed to use a baseline study with chemical and biological data at each port. In this this thesis, the regulations and available technologies for the treatment of ballast tanks were summarized. The aim of the thesis was to determine the concentrations of faecal and total coliform bacteria in the estuary of the river Rižana, which is the location of the main port, two other pools in Koper bay and at the reference station in the outer part of the Bay of Koper. The analyses of faecal coliforms were performed by the membrane filtration method using different growth media, that are recommended for coliforms bacteria analysis. The results of the faecal coliforms in the sea water samples shows high concentrations at the sampling site in the estuary of the river Rižana, where the outlet of the waste water from the treatment plant Koper is located. Microbiological results of faecal coliforms in sediment samples differ, but high levels were detected at all sampling sites. A preliminary study was performed comparing species composition of total bacterial communities in samples of water and sediment from different sampling sites in the Gulf of Koper using the method of denaturing gradient gel electrophoresis.