The relationship between aquaculture activities and water quality plays an important role in determining the volume and quality of production as well as the impact of aquaculture on the aquatic environment. The natural assimilation capacity of a waterbody is often insufficient to cope with the continuous input of wastes from fish farms. Their impact depends not only on the waste itself, but also on other factors such as the local hydrodynamics at the farm site or the cultured species’ feeding pattern. We combine a hydrodynamic model with a transport code to simulate the deposition of fecal pellets and uneaten feed from a gilthead seabream farm in the western Mediterranean Sea. The simulation spans a full 17-month rearing cycle and considers the natural variations in the feed demand of the fish during this period. The results indicated that the maximum benthic concentrations of organic matter and nutrients were found within a 100–500 m distance from the cages, depending on the type of particulate waste and on the local current characteristics. The combination of a long simulation period and realistic hydrodynamic patterns highlights the importance of considering long-term current variability when assessing the environmental impact of fish farms, and stresses the limitations of current simplistic assessment practices.