The Laurentian Great Lakes have experienced unprecedented ecological and environmental changes, especially after the introduction of invasive quagga mussel (Dreissena rostriformis bugensis). While impacts on ecological functions have been widely recognized, the response of carbon dynamics to invasive species remains largely unknown. We report new CO2 data showing significant increases in pCO2 (up to 800 μatm in Lake Michigan) and CO2 emission fluxes in most of the Great Lakes compared to those prior to or during the early stage of the colonization of invasive quagga mussels. The increased CO2 supersaturation is most prominent in Lakes Huron and Michigan, followed by Lakes Ontario and Erie, but no evident change was observed in Lake Superior. This trend mirrors the infestation extent of invasive quagga mussels in the Great Lakes and is consistent with the decline in primary production and increase in water clarity observed pre- and post-Dreissena introduction, revealing a close linkage between invasive species and carbon dynamics. The Great Lakes have become a significant CO2 source to the atmosphere, emitting >7.7 ± 1.0 Tg-C annually, which is higher than the organic carbon burial rate in global inland-seas and attesting to the significant role of the Laurentian Great Lakes in regional/global CO2 budget and cycling.