Dense aquatic weed mats are likely to enhance oxygen depletion and build-up of organic matter. As a result of a thick biomass layer, water flow is reduced and hypoxic conditions prevail; the imbalance between aerobic and anaerobic processes can influence the net ecosystem metabolism and its carbon budget. We here present results from a multi-year investigation (2013-2015) carried out on a mesotrophic shallow lake of south-west of France (Lacanau Lake), where 10% of surface is occupied by dense beds of Egeria densa and Lagarosiphon major. Investigations were carried out through multiple approaches, such as 24h-cycle water collection, GIS mapping, growth rates measurements and sedimentary organic matter assessment. Results from this study revealed that, thanks to advantageous hydrodynamics local conditions (strong wind), those plants do not necessarily trigger water stagnation and hypoxia. Nevertheless, their fast growth generates the accumulation of a huge quantity of labile litter, which feeds respiration processes and methanogenesis on the bottom of the macrophytes bed. Our study underlines that dense aquatic weed mats may constitute important hotspots for greenhouse gases emissions at our latitude, notably enhanced by mild temperature and strong irradiation all over the year.