In this study, a human operator (helmsman) controls a ship as continuous system manually according to captain’s command against to random disturbances through bosphorus of Istanbul and it’s investigated how their behaviour affects the course and coordinates of th ship. For this working, participated to navigation on bosphorus with different type vessels especially longer than 120 meter and determined where regions are dangerous and have risks. Despite all vessels have modern navigation devices, it’s forbidden to use autoplot and they have to control their vessels manually according to rules [2]. The purpose of this study is to compare with autoplot navigation and manual navigation on bosphorus and present the cause of why autoplot is forbidden with scientific data