This study examined the carbon footprints of freshwater fish farming and Euryale ferox seed (gorgon fruit) production, comparing integrated ecological mode and traditional farming practices based on ISO 14067 and PAS 2050 standards. The ecological mode achieved a 24% lower carbon footprint per unit product than traditional practices, driven by reduced material and energy use. Key emission sources included aeration electricity, feed, and wastewater treatment for fish farming, fertilizers, insecticides, and drainage energy for E. ferox planting. The integrated model combining high-density fish ponds and E. ferox pond reduced the overall carbon footprint (Micropterus salmoides: 4.342 kg CO₂-eq/kg; E. ferox seed: 0.208 kg CO₂-eq/kg) compared to traditional practices (Micropterus salmoides: 5.672 kg CO₂-eq/kg; E. ferox seed: 0.297 kg CO₂-eq/kg). It also lowered production costs, increased profits, and mitigated GHG emissions by using E. ferox and lotus ponds as treatment facilities and reducing fertilizer use. The ecological model showed lower unit costs and higher profits (Micropterus salmoides: 4.01 RMB/kg vs. 2.46 RMB/kg; E. ferox seed: 2.53 RMB/kg vs. 1.93 RMB/kg) than those of the traditional mode. This study underscores the potential of ecologically integrated modes to mitigate water pollution and carbon emissions in agriculture, offering a sustainable solution to meet the rising demand for aquatic products.