In spite of commonly held view of streams as well-oxygenated habitats, we found both surface and interstitial water to be supersaturated with methane compared to the atmosphere at all five localities (Mach et al. in review). Availability of interstitial habitats for bacteria and archaea carrying out anaerobic processes has been confirmed by our previous (Hlavacova et al. 2005, 2006; Cupalova & Rulik 2007) and contemporary findings. During this study we found relatively well developed populations of methanogenic archaea at all localities and that all localities also showed positive methanogenic potential. Emissions of methane from water ecosystems results from complex microbial activity in the carbon cycle (production and consumption processes), which depends upon a large number of environmental parameters such as availability of carbon and terminal electron acceptors, flow velocity and turbulence, water depth. In our previous paper (Hlavacova et al. 2006), we suggested that surface water concentrations, and as a consequence methane gas emissions to the atmosphere would result from downstream transport of gases by stream water (advection in/out), and moreover, from autochthonous microbial metabolism within the hyporheic zone. If so, surface water is continually saturated by gases produced by hyporheic metabolism, leading to supersaturation of surface water and induced diffusion of these gases out of river water (volatizing). Moreover, the run-off and drainage of adjacent soils can also contribute greatly to the degree of greenhouse gas supersaturation (De Angelis & Lilley 1987, Kroeze & Seitzinger 1998, Worral & Lancaster 2005, Wilcock & Sorrell 2008). For example, CH4 in the estuarine waters may come from microbial production in water, sediment release, riverine input and inputs of methane-rich water from surrounding anoxic environments (Zhang et al. 2008b). For the European estuaries, riverine input contribute much to the estuarine CH4 due to high CH4 in the river waters and wetlands also play important roles. However, low CH4 in the Changjiang Estaury (China) may be resulted from the low CH4 in the Changjiang water together with the low net microbial production and low input from adjacent salt marshes (Zhang et al. 2008b). Dissolved methane concentrations in a surface water of Sitka stream is consistent with literature data on methane in rivers published by Middelburg et al. (2002) and Zhang et al. (2008b).