Production of methane and carbon dioxide as well as methane concentrations in surface waters and emissions to the atmosphere were investigated in two flow-through lake complexes (Uzlina–Isac and Puiu–Rosu–Rosulet) in the Danube Delta during post-flood conditions in May and low water level in September 2006. Retained nutrients fuelled primary production and remineralisation of bioavailable organic matter. This led to an observable net release of methane, particularly in the lakes Uzlina, Puiu and Rosu in May. Input from the Danube River, from redbuds and benthic release contributed to CH4 concentrations in surface waters. In addition to significant river input of CO2, this trace gas was released via aerobic remineralisation within the water column and in top sediments. Emission patterns of CO2 widely overlapped with those of CH4. Generally, greenhouse gas emissions peaked in the lake complex adjacent to the Danube River in May due to strong winds and decreased with increasing hydrological distance from the Danube River. Intense remineralisation of organic matter in the Danube Delta lakes results in a net source of atmospheric greenhouse gases.