The physicochemical sediment and interstitial water properties of the investigated sites showed large horizontal and vertical gradients. Sediment grain median size decreased along a longitudinal profile while organic carbon content in a sediment fraction < 1 mm remained unchaged (Table 2). Generally, interstitial water revealed relatively high dissolved oxygen saturation with the exceptions of localities IV and V where concentration of dissolved oxygen sharply decreased with the depth, however, never dropped below ~ 10%. Vice versa, these two localities were characterized by much higher concentrations of ferrous iron and dissolved methane (Table 2) compared to those sites located upstream. Concentration of the ferrous iron reflects anaerobic conditions of the sediment and showed the highest concentration to occur in the deepest sediment layers (40-50cm). Average annual temperatures of interstitial water at localities in downstream part of the Sitka stream were about 2.5 oC higher compared to localities upstream and may probably promote higher methane production occuring here. Precursors of methanogenesis, acetate, propionate and butyrate were found to be present in the interstitial water at all study sites, however, only acetate was measured regularly at higher concentration with maximum concentration reached usually during a summer period.