Almost every scientific or industrial field today longs for an interdisciplinary approach to tackle, analyse and solve the problems at hand. It is clear that many studies designed as a basis for project documentation or any other type of study do not make sense if only the benefit of improving a single part of the observed ecosystem, e.g. through construction measures, is considered. Nowadays, both computational resources as well as modelling techniques and approaches are constantly evolving. Moreover, these resources are the most cost-effective approach for analysing and solving different types of problems. One of these problems is certainly ballast water management and related issues. The discharge of ballast water and the subsequent spread of non-native and potentially invasive species pose a serious threat to the marine environment into which they are introduced. In addition, the above processes can lead to a number of unfavourable consequences for the economy, biodiversity and overall quality of life of a system of which the marine environment is a part. Among the novel modelling approaches that take into account the interdisciplinarity between research fields, the application of agent-based models (referred to as ABM in the following text) certainly stands out as a tool that can be successfully used for the analysis of various problems. ABM makes it possible to model the dynamics of complex adaptive systems that are characterised by the possibility of self-organisation and create a certain hierarchy between the stakeholders of the modelled system. Such a system consists of autonomous and interactive agents whose behaviour is tracked within the modelled environment. Agents and the environment are two of the three elements that make up any ABM. The third element is the interactions between the agents and the interactions between the agents and the environment. The latter element is represented by the mathematical equations that describe the behaviour of the agents, taking into account the other agents in their environment and the changes in their environment. In general, ABM is applied to topics where it is necessary to take into account the stochasticity of the prevailing processes, objects or individuals that cause changes in the analysed system. These topics therefore range from the analysis of consumer and stock markets to the analysis of ecosystems, biological processes and the modelling of sociological phenomena. As part of this research, ABM has been applied to problems related to coastal engineering. Specifically, ABM has been applied to describe the secondary spread of alien species introduced into harbours via ballast water. An original ABM of planktonic dispersal, coupled with a calibrated 3D hydrodynamic model (hereafter referred to as HD) of sea circulation, was developed to define dispersal patterns as a function of meteorological, hydrological and oceanographic conditions in port areas. Two Croatian ports (Ploče and Rijeka) were considered in terms of spatial extent, where the field measurements of sea currents and the analysis of available static and dynamic input data were carried out. For each of the areas, a new HD model of the sea current was developed, calibrated and checked against the field measurements. The developed HD models take into account the finite volume method based on the solution of the governing Navier-Stokes equations in the MIKE 3 FM module. A total of four acoustic Doppler current profilers (referred to as ADCPs in the following text) were bottom mounted inside the port area over two measurement periods (two ADCPs per port). The measurements were carried out as part of the project “Development of system for control and protection of ports from introduction of alien species” (ProtectAS) and included the recording of current velocity, sea level dynamics and sea temperature at the depths of the measuring instruments. The time periods of the field measurements correspond to the numerical simulations considered, with the first period being between October 2020 and January 2021 and the second between July and October 2021. The first period is autumn/winter (referred to as A/W in the following text), which covers the oceanographic conditions characterised by the absence of vertical stratification of the sea column. The second period is summer/early autumn (referred to as S/A in the rest of the text), when stratification is present in all parts of the area under consideration. As for the dominant circulation generators, the intense sea currents in both areas are mainly driven by the effect of the wind at the sea-atmosphere boundary. However, for the modelling of the circulation in the port of Ploče area, the effects of the inflow from the Neretva and Baćinska Lakes were taken into account. This was the crucial inclusion of boundary conditions that were neglected in previous studies, especially during the A/W period of the simulation when the highest discharges are expected. Calibration of the HD model was performed for the A/W period and validation for the S/A period by comparing the modelled and measured time series of sea level dynamics as well as the U and V velocity components at different depths and at the locations of the ADCPs. Achieving a satisfactory level of confidence in the HD model ultimately led to the establishment of a solid basis for further analysis of the modelling of the spread of alien species originally introduced into the port area by the ballast water discharge. The spread of the modelled non-native species after their introduction into the model domains was analysed by coupling the calibrated HD model with an ABM of phyto- and zooplankton movement. In this dissertation, original ABMs were developed to analyse the patterns of horizontal and vertical transport of the modelled plankton fractions that occur as a result of the dynamics of the prevailing meteorological, hydrological and oceanographic conditions. A total of three fractions were modelled, namely diatoms and dinoflagellates (representatives of phytoplankton) and copepods (representatives of zooplankton). The selection of the plankton fractions itself is not random, but one of the results of the ProtectAS project. Based on field samples and laboratory analyses, it was determined that diatoms and dinoflagellates dominate in the phytoplankton samples and copepods in the zooplankton samples in all measurement periods. The movements of the modelled fractions are described by mathematical and logical formulae defined on the basis of previous laboratory studies. ABMs were implemented through the development of MIKE ECO Lab templates with the included ABM Lab module. Within the developed ABM, a scientific contribution was made compared to previous research by defining mathematical expressions for the movement of plankton fractions vertically through the sea column as a function of environmental stimuli (3D field of sea temperature and light intensity at particle depth). Based on the relationship between the environmental conditions and the current patterns, a proposal is made for operational measures of ballast water management when the arrival of a vessel intending to empty the ballast tank in harbour is announced. The operational measures consist of informing the ship of a change of discharge location or delaying the discharge of ballast water until such environmental conditions occur that the sea circulation does not lead to significant secondary dispersion. In addition, guidelines for the ballast water management of ships have been developed as part of this research, which include the operational measures mentioned above. The guidelines themselves are described in terms of three implementation phases (preparatory measures, operational measures, measures after implementation of the measures) and are primarily determined by taking into account the prevailing environmental conditions at the time of ballast water discharge and the time after discharge based on available forecasts of meteorological, hydrological and oceanographic parameters characterising the circulation field in the port. Through guidelines with operational measures adopted based on the results of simulations of the combined HD circulation model and ABM transport, it is possible to reduce the spatial extent of the secondary spread of potentially invasive species introduced by the ballast water of ships.