Seagrass beds are crucial marine habitats with valuable ecosystem functions, such as carbon storage and nutrient cycling. Unfortunately, human activities that alter the natural environment can have detrimental effects on these ecosystems. The most significant change humans have made in the Earth system is the increase in the availability of phosphorus and nitrogen, which are essential for seagrass growth. This increase can also lead to enhanced growth of epiphytic algae and elevated microbial activity, driven by the increased availability of labile carbon. However, the changes in ecosystem scale carbon cycling resulting from these modifications are not yet fully understood. To address this, we used stable isotope (13C) labeling to trace the production, transformation, and fate of carbon in both nutrient-enriched and non-enriched seagrass ecosystems. By understanding the effects of human alterations on carbon cycling, we can make informed decisions on how to protect seagrass ecosystem functioning.