<p>The expansion and development of aquaculture activities in the Tam Giang–Cau Hai lagoon system, including the Thuy Tu and Cau Hai lagoons, has generated waste that impacts the natural environment. This research focused on assessing the isotopic compositions of carbon and nitrogen in suspended organic matter within the aquaculture ponds and surrounding ecosystems of the Thuy Tu and Cau Hai lagoons. The isotopic fingerprints of organic carbon and nitrogen in suspended matter showed significant differences between the Thuy Tu and Cau Hai lagoons, depending on the sampling period (March and July). The ratio of particulate organic carbon to particulate nitrogen (POC/PN) in suspended matter indicated a substantial contribution from phytoplankton. A mixing model was applied to determine the impact of aquaculture waste on the Thuy Tu and Cau Hai lagoons. By quantifying the contributions of each carbon and nitrogen source, this study successfully evaluated the significant influence of artificial fertilizer source on both lagoons for the first time. Fertilizer contributions relating to aquaculture activities increased progressively with distance in Thuy Tu lagoon, while in the Cau Hai lagoon, the impact of fertilizers came from both aquaculture activities and agricultural production.</p> Graphical Abstract <p></p>