Seagrass ecosystems are important carbon sinks in the coastal zone, aiding climate change mitigation by sequestering carbon dioxide from the atmosphere. Shifts in the ability of seagrass ecosystems to bury and preserve carbon have the potential to alter the global carbon balance. A major impact on seagrass ecosystems is the influx of anthropogenic nutrients into coastal waters. In coastal ecosystems, elevated nutrient concentrations can cause an increase in labile organic carbon, increased methane emissions, and loss of stored carbon via priming effects during high levels of microbial activity. To investigate the effects of nutrient enrichment on the seagrass carbon budget, we fertilized seagrass beds with artificial slow-release nutrients for ten weeks and conducted benthic incubations to measure sediment-water fluxes of oxygen, methane, dissolved inorganic and organic carbon, and dissolved radiocarbon. Nutrient enrichment increased daytime primary production and night-time respiration rates, indicating heightened microbial activity that could release stored carbon. However, methane emissions were lower in fertilized seagrass, highlighting the ability of seagrass to buffer potential adverse effects of nutrient enrichment. Understanding how nutrient enrichment may alter the carbon storage capacity of seagrass beds is imperative for predicting their role as "blue carbon" ecosystems in the face of environmental changes.