The increase in atmospheric methane concentration, which is determined by an imbalance between its sources and sinks, has led to investigations of the methane cycle in various environments. Aquatic environments are of an exceptional interest due to their active involvement in methane cycling worldwide and in particular in areas sensitive to climate change. Furthermore, being connected with each other aquatic environments form networks that can be spread on vast areas involving marine, freshwater and terrestrial ecosystems. Thus, aquatic systems have a high potential to translate local or regional environmental and subsequently ecosystem changes to a bigger scale. Many studies neglect this connectivity and focus on individual aquatic or terrestrial ecosystems. The current study focuses on environmental controls of the distribution and aerobic oxidation of methane at the example of two aquatic ecosystems. These ecosystems are Arctic fresh water bodies and the Elbe estuary which represent interfaces between freshwater-terrestrial and freshwatermarine environments, respectively. Arctic water bodies are significant atmospheric sources of methane. At the same time the methane cycle in Arctic water bodies is strongly affected by the surrounding permafrost environment, which is characterized by high amounts of organic carbon. The results of this thesis indicate that the methane concentrations in Arctic lakes and streams substantially vary between each other being regulated by local landscape features (e.g. floodplain area) and the morphology of the water bodies (lakes, streams and river). The highest methane concentrations were detected in the lake outlets and in a floodplain lake complex. In contrast, the methane concentrations measured at different sites of the Lena River did not vary substantially. The lake complexes in comparison to the Lena River, thus, appear as more individual and heterogeneous systems with a pronounced imprint of the surrounding soil environment. Furthermore, connected with each other Arctic aquatic environments have a large potential to transport methane from methane-rich water bodies such as streams and floodplain lakes to aquatic environments relatively poor in methane such as the Lena River. Estuaries represent hot spots of oceanic methane emissions. Also, estuaries are intermediate zones between methane-rich river water and methane depleted marine water. Substantiated through this thesis at the example of the Elbe estuary, the methane distribution in estuaries, however, cannot entirely be described by the conservative mixing model i.e. gradual decrease from the freshwater end-member to the marine water end-member. In addition to the methane-rich water from the Elbe River mouth substantial methane input occurs from tidal flats, areas of significant interaction between aquatic and terrestrial environments. Thus, this study demonstrates the complex interactions and their consequences for the methane distribution within estuaries. Also it reveals how important it is to investigate estuaries at larger spatial scales Methane oxidation (MOX) rates are commonly correlated with methane concentrations. This was shown in previous research studies and was substantiated by the present thesis. In detail, the highest MOX rates in the Arctic water bodies were detected in methane-rich streams and in the floodplain area while in the Elbe estuary the highest MOX rates were observed at the coastal stations. However, in these bordering environments, MOX rates are affected not only via the regulation through methane concentrations. The MOX rates in the Arctic lakes were shown to be also dependent on the abundance and community composition of methane-oxidising bacteria (MOB), that in turn are controlled by local landscape features (regardless of the methane concentrations) and by the transport of MOB between neighbouring environments. In the Elbe estuary, the MOX rates in addition to the methane concentrations are largely affected by the salinity, which is in turn regulated by the mixing of fresh- and marine waters. The magnitude of the salinity impact on MOX rates thereby depends on the MOB community composition and on the rate of the salinity change. This study extends our knowledge of environmental controls of methane distribution and aerobic methane oxidation in aquatic environments. It also illustrates how important it is to investigate complex ecosystems rather than individual ecosystems to better understand the functioning of whole biomes.