Sediments were collected in three small water courses upstream and downstream a water treatment plant discharge, in one highly fertilized eutrophic pond, and from one oligotrophic brook. They were analysed for ammonium oxidation activity, for nitrite oxidation activity and for their respective nitrifying community size. The relationships between variables was investigated by a principal components analysis of the physicochemical and biological data.Upstream sites of treatment plant discharges looked similar to an oligotrophic river, but the downstream sites have certain similarities with a highly eutrophic pond. Globally, whatever the hydrosystem, the organic carbon and organic nitrogen content of the sediments were highly correlated with nitrifying activity and nitrifiers number (significance level α = 0.001), but there was no significant correlation between the nitrifiers number and the related activity. The hypothesis of a role of the grain size on the nitrification communities was tested. A Mann-Withney U test (α = 0.05) indicated that, whatever the sediment, the two fractions of sand (500-200 µm and 200-50 µm) were non significantly different for nitrification. Conversely, the silt-clay fraction was significantly different from sands for all the nitrification's parameters. This silt-clay fraction exhibited the highest functional nitrifying community per mass unit indicating that the silt fraction is a main contributor to the nitrification process in river sediment. Finally, for each river, there were significant differences (at α = 0.05) between the nitrifiying communities in downstream and upstream sediments. In the 3 studied rivers, upstream sites were significantly higher in terms of activity and in terms of number of nitrifying bacteria. The effect of wastewater effluents discharge seems to be site specific.