Abstract Two freshwater sediments (organic-poor and organic-rich) that contained their distinct natural microbial communities were incubated in experimental microcosms with either NH(4) (+) or NO(2) (-) in the overlying water. Microsensor measurements revealed the thin oxic surface layer as a site of initially high rates of nitrification, i.e. O(2), NH(4) (+), and NO(2) (-) consumption, and NO(3) (-) production. Unexpectedly, during the subsequent 4-week incubation NH(4) (+) consumption decreased in both sediment types and NO(2) (-) consumption decreased in the organic-rich sediment. In the organic-rich sediment O(2) consumption and NO(3) (-) production paralleled these decreases, i.e. the reduced NH(4) (+) and NO(2) (-) consumption rates were most probably due to reduced activity of nitrifiers. These microsensor data imply factors other than frequently suggested competition between nitrifiers and heterotrophs for NH(4) (+), NO(2) (-) or O(2) as causes for the loss of nitrification activity. We hypothesize that experimental manipulations (e.g. removal of macrofauna, redistribution of particulate organic matter, permanent nutrient enrichment) rendered the performance of the microbial community unstable. It is thus recommendable to restrict experiments in such commonly used model systems to the period of highest stability.