In aquaculture, it is crucial to understand and mitigate the carbon footprint for sustainable production. As demand for seafood increases, various production techniques compete for an eco-friendly status. This review examines the carbon footprint of various land-based marine aquaculture systems, highlighting their environmental impact. Through exploring innovations and best practices, it navigates the complexities of reducing emissions and promoting carbon sequestration. Some proposals for this purpose are based on diversification through low-trophic-level species, the preservation of high-carbon sequestration sites, polyculture, organic aquaculture and improvements in nutrition, feeding, waste and energy management. In this sense, some land-based aquaculture systems are progressively adapting and updating their zootechnical procedures. Recirculating Aquaculture Systems (RASs) offer interesting advantages such as water conservation, pollution reduction and biosecurity. Integrated Multi-Trophic Aquaculture systems (IMTAs) aim to address two major issues in aquaculture: efficient water usage and the environmental impact of effluents, which are rich in organic particles and dissolved nutrients from undigested food and feces; hence, these systems involve cultivating multiple species (polyculture). Biofloc Technology (BFT) is based on the formation of bioflocs in a culture medium. These systems can enhance feeding efficiency and waste management, thus optimizing nutrient utilization and minimizing environmental impact, achieved through reduced water and fertilizer usage. Traditional (extensive) aquaculture systems operate with minimal input of feed and chemicals, relying heavily on the natural productivity of the ecosystems; thus, the need for manufactured feed, the environmental impact associated with feed production and the transportation and overall costs are significantly reduced. Overall, while RASs, BFT and extensive systems in general offer significant sustainability benefits, IMTA’s holistic approach to ecosystem management and nutrient recycling makes it, in our estimation, the most effective method in terms of ecological footprint in aquaculture. However, its quantitative evaluation is extremely complex, and there is currently a lack of references about its global carbon footprint. Therefore, further research and development are required, as well as collaboration and knowledge-sharing among stakeholders.