We here present an overview and the first results of our studies focusing on Charophytes, and our research plans dedicated to this algal group. Charophyte species such as Nitella confervacea, Chara fragifera, Nitella translucens, Nitella hyalina and Chara globularis are abundant and frequent in the Aquitaine region (SW France, Bay of Biscay), where a chain of shallow lakes stands just behind the coastal dunes. These lakes are characterized by a sandy bottom, low alkalinity and an asymmetric bathymetry from the west to the east side. Since 2011, Charophytes distribution is assessed in these lakes, by means of echosounding and point intercept transects along orthogonal grids. Since 2013, macrophyte assemblages and co-occurrence are assessed by quadrats to test the influence of local hydromorphological features. Concomitantly, net ecosystem metabolism is assessed on sandy patches colonized in part by Charophytes, for the measurement of dissolved gases and nutrients (O2, CO2, CH4, DIN) benthic fluxes. Preliminary results show that Charophytes often occur with isoetid plants such as Lobelia dortmanna and Littorella uniflora, preferentially colonizing poor-organic sediments and wind-exposed shores. Our studies also highlight the potential role of these macroalgae and associated bacterial guilds on methane oxidation at the sediment-water interface, showing the intrinsic value of Charophytes for shallow lakes ecosystem functioning.