A contaminant is a chemical or biological substance in a concentration that can potentially cause adverse effects on the physical, chemical, or biological properties of a water body. Contamination of surface water bodies poses serious risks to both aquatic ecosystems and human health. In this respect, hydrodynamic modeling is an essential method to study scenarios for hydroenvironmental problems, such as the impact of marine pollutants in coastal areas. In the framework of the Interreg Italy-France Maritime Cooperation Project Wastewater Management for the improvement of the harbor water quality, GEREMIA, this study numerically implements such a concept on Genova (Italy) harbor using a world-leading 3D modeling suite, Delft3D to investigate the hydrodynamics and transport process within these ports.