The environmental effects of ship propellers were not even close to fully examined before the current massive ships were introduced to sea trade. Larger ships, result in greater length, beam, draft and propulsion power. Of concern here is the under-keel clearance (UKC) and applied power, the most important parameters causing sea bottom sediment resuspension and, consequently, the transport and deposition of washed sediments. The problems are multifarious: shorelines could be contaminated with heavy metals, petroleum hydrocarbons and other organic chemicals, which are sometimes buried deep in the sediment bed. The effects of resuspension on marine life have been well documented by marine biologists. Further, a ship passing through a flow field may have a significant hydrodynamic effect on the shipping channel: waves generated by moving vessels can accelerate shoreline erosion; erosion around quay piles have a negative impact on sea flora. Waves can also affect other manoeuvring vessels or ships at berth. Available empirical models are applicable for a steady state condition, addressing velocity and, consequently, shears at the sea bottom for defined UKC and states of applied power. The idea here is to calculate material resuspension dynamically in the water column based on realistic manoeuvring conditions, which can be a matter of some complexity. During a manoeuvre, the pilot must bring the ship into or out of the harbour in the safest possible way, operating the telegraph, rudder, thrusters and possibly tugs, and also co-ordinating the work of the linesmen. The jet speed powering the vessel is not only a function of the speed of the propeller, but also of the present speed of the ship, which has an effect on the propeller’s constantly changing torque. Additionally, the bathymetry is constantly changing, and the streamlines hit not only the seabed, but also the bank and other structures of the harbour basin. The resuspended material remains in the column long after the ship has finished manoeuvring, moving slowly through the entire water column and being transported not only by the remaining streamlines of the ship but also by general currents. Realistic manoeuvring parameters can be obtained from real-time simulations with a real crew using state-of-the-art Full Mission Bridge Simulators (FMBS); eddies and the like contribute to the distribution and material resuspension and can be calculated by applying numerical modelling. In this paper, a container ship departure manoeuvre is simulated dynamically using Wartsila FMBS obtained data, which are postprocessed and coupled with the MIKE 3 FM hydrodynamic modelling application to which we add the precise port of Koper bathymetry to gain ship propeller spatial jet velocity distribution in specific time domains. Obtained jet velocity distribution is further coupled with the MIKE 3 MT particle tracking application to visualize total resuspended sediment transport patterns, etc. Container ships were selected to amplify the urgency of this phenomenon; they are the most intrusive in terms of resuspending and scouring the seabed given their powerful engines and larger propellers. Passenger ships could have been used, car carriers, or even tankers; but the fear among scientists is that the issue will not be taken seriously enough by certain stakeholders.