<p>Aquatic primary producers, including submerged macrophytes and cyanobacteria, play essential roles in lake ecosystems by maintaining water quality and driving carbon cycling. However, the impact of their decomposition on greenhouse gas (GHG) emissions and nutrient dynamics remains poorly understood. This study examines how the decomposition of cyanobacteria and three submerged macrophyte species (<i>Ceratophyllum demersum</i>, <i>Vallisneria natans</i>, and <i>Potamogeton wrightii</i>) influences GHG emissions and nutrient cycling in lake systems. Over a 117-day period, microcosms were used to monitor decomposition and measure the release of methane (CH₄), carbon dioxide (CO₂), nitrogen, and phosphorus. Emission trends and water quality changes were modeled using the Generalized Additive Model, and the relationships between GHG emissions and nutrient release were analyzed. Our results indicate that cyanobacterial decomposition significantly increased GHG emissions and nutrient release. By day 25, the CH₄ emissions in the cyanobacteria treatment were 1.37 to 1.89 times higher than in the submerged macrophyte treatments, while final concentrations of nitrogen-related nutrients in the water column were 5.90 to 7.67 times greater. Among the submerged macrophytes, slight differences were observed in GHG emissions and nutrient release: <i>Vallisneria natans</i> exhibited a lower CO₂ release rate, while <i>Ceratophyllum demersum</i> showed reduced phosphorus release. These findings suggest that certain submerged macrophytes, particularly <i>Vallisneria natans</i> and <i>Ceratophyllum demersum</i>, can mitigate GHG emissions and regulate nutrient cycling. Promoting their growth may therefore serve as an effective strategy for lake restoration and eutrophication management. However, field validation and long-term monitoring are needed to assess their practical effectiveness and ecological stability under natural conditions.</p> Graphical Abstract <p></p>