Nitrogen dynamics were investigated in the top centimeters of bottom sediment in three different geomorphologic units (riffles, sand bars, pools) and along two contrasted reaches (nitrogen-rich, nitrogen-poor) of a rural stream. Some predictions of links between geomorphology and processes were verified: (i) hydrological exchanges and nitrification were lower in pools than in riffles and bars, whereas (ii) ammonification and denitrification were higher in pools. Studies of denitrification potential in six other reaches of three N-rich streams support these conclusions and demonstrate that pools are spots of high microbial activity in streams.