Abstract: Submerged macrophytes play a vital role in the carbon cycling of lake ecosystems. However, the extent to which contrasting macrophyte growth forms—bottom-dwelling versus canopy-forming—control annual CO₂ and CH₄ emissions is unresolved, limiting evidence-based guidance for lake restoration aimed at carbon mitigation. We conducted a fully replicated, year-long outdoor mesocosm experiment under natural temperature and light regimes to quantify greenhouse gas fluxes from monospecific stands of four widespread macrophytes: bottom-dwelling Vallisneria denseserrulata and canopy-forming Ceratophyllum demersum, Myriophyllum spicatum and Hydrilla verticillata. Monthly diffusive flux measurements were integrated with high-resolution data on water chemistry, macrophyte biomass, zooplankton, phytoplankton and the functional genes mcrA and pmoA for methanogenic and methanotrophic communities. Canopy-forming macrophytes reduced annual CO₂ fluxes by 5–13 mol m⁻² yr⁻¹ relative to bottom-dwelling treatments, with Hydrilla and Myriophyllum systems functioning as net carbon sinks (negative CO₂-equivalent balance), whereas Vallisneria and Ceratophyllum remained sources. Canopy-forming macrophytes exhibited higher biomass than bottom-dwelling forms, enabling greater nutrient uptake and correspondingly higher CO₂ fixation via photosynthesis. CH₄ release was strongly modulated by plant biomass and associated redox conditions. These results demonstrate that canopy-forming macrophytes offer superior potential for CO₂ mitigation and CO₂-equivalent balance, providing essential tradeoff information for managers selecting plant assemblages for climate-smart lake restoration

Key words: lake, submerged macrophyte, growth forms, greenhouse gas, diffusive flux