This study compares the farm management model used in the Mediterranean gilthead seabream (GHSB; Sparus aurata) industry (S1)—stepped entry of juveniles throughout the year with several production cycles and fish ages overlapping in a single farm—with that used in the salmon industry (S2)—the whole is farm filled with fish that are the same age at once with a fallowing period between rearing cycles—in terms of waste production by coupling digestibility coefficients with growth, feeding, and eating behavior models into a mass balance model. We considered the total C, N, and P content in the different waste fractions (particulate and dissolved wastes). The model, which simulated real farming conditions, showed relevant quantitative and qualitative differences between both strategies, with stocked biomass and water temperature as the main drivers, the amount of feed wasted by chewing as the most relevant fraction differentiating both strategies, and the fallowing period as the main distinguishing management feature. We discuss the influence of both farming strategies on some key performance and environmental aspects, such as benthic recovery, the breakdown of the life cycle of pathogens, and adaptability to climate change. Our results suggest that changing the GHSB industry’s production model is necessary for its sustainability.