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Remote monitoring and flow cytometry were lately significantly developed. Ballast water treatment systems (BWTS) are in use on lot of ships today and new systems are still in research projects worldwide as well. So fast development requires control and monitoring of installed systems. International Maritime Organization (IMO) regulations and Ballast Water Convention 2004 include inspection of treated ballast water (BW) if needed. That could initiate lot of legal, beside to operational, problems in maritime industry. That implicates the need of a monitoring treated BW before the ship enters a port. It has been described in this article how to monitor treated ballast water to make sure the BW and BWTS on a ship is in proper condition, but before the port entrance. The monitoring system and its parts flow cytometer and satellite communication system together with remote operation system from the land office have been explained. Auto-monitoring of treated BW on board by using newest sensor technologies and satellite communications are included in the model of three sub-systems and remote operation from the land office, but to be autonomous from the ship's crew. Main goal of the research is that a ship enters the port with the BW cleanliness confirmation. In this way there is no need to sample the BW and no time is lost for analysing the samples.