Exotic hydrophytes are often considered as aquatic weeds, especially when forming dense mats on an originally poorly-colonized environment. While management efforts and research are focused on the eradication and/or on the impacts on the biodiversity, their influence on ecosystem functioning of shallow lakes is still poorly explored. Indeed, as a result of a thick biomass layer, plants may reduce water flow and trigger hypoxic conditions; the imbalance between aerobic and anaerobic processes may then affect the net ecosystem metabolism and its carbon budget. We here present results from a multi-year investigation (2013-2016) carried out on two mesotrophic shallow lakes of south-west of France (Lacanau and Parentis-Biscarrosse Lakes), 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, growth rates measurements and oxygen high-frequency probe measurements. Results from this study revealed that, thanks to advantageous hydrodynamics local conditions (i.e. frequent and strong wind), those plants do not systematically trigger water stagnation and hypoxia. Also, their fast growth implies the exhaustion of carbon and nutrients naturally occurring in the water. Within the plants bed, biomass senescence generates the build-up of a huge quantity of labile litter, which feeds respiration processes and nutrients regeneration from the sediment. Our study suggests that aquatic weeds may perform as ecosystem engineers, by acting on local hydrology and by stimulating nutrients regeneration. Still, the ultimate fate of sedimentary organic matter is to define, as well the role of colonized sites in enhancing whole-lake carbon emissions.