The Achères wastewater treatment plant, located just downstream of Paris, discharges its effluents into the lower Seine River. The effluents contain large numbers of heterotrophic bacteria, organic matter, and ammonium and are a source of nitrifying bacteria. As a result, degradation of organic matter by heterotrophic bacteria and subsequent oxygen depletion occur immediately downstream of the effluent outlet, whereas nitrifying bacteria apparently need to build up a significant biomass before ammonium oxidation significantly depletes the oxygen. We quantified the potential total nitrifying activity and the potential activities of the ammonia- and nitrite-oxidizing communities along the Seine River. In the summer, the maximum nitrifying activity occurs in the upper freshwater estuary, approximately 200 km downstream of Achères. The quantities of nitrifying bacteria, based on amoA gene copy numbers, and of Nitrobacter organisms, based on 16S rRNA gene copy numbers, were correlated with the potential nitrifying activities. The species composition of ammonia-oxidizing bacteria was investigated at two sites: the Triel station just downstream from Achères (km 84) and the Seine freshwater estuary at the Duclair station (km 278). By means of PCR primers targeting the amoA gene, a gene library was created. Phylogenetic analysis revealed that the majority of the analyzed clones at both sites were affiliated with the genus NITROSOMONAS: The Nitrosomonas oligotropha- and Nitrosomonas urea-related clones represented nearly 81% of the community of ammonia-oxidizing bacteria at Triel and 60% at Duclair. Two other ammonia-oxidizing clusters of the beta subclass of the Proteobacteria, i.e., Nitrosomonas europaea- and Nitrosospira-like bacteria, were found in smaller numbers. The major change in the ammonia-oxidizing community between the two stations along the Seine River-upper estuary continuum was the replacement of the N. oligotropha- and N. urea-related bacteria by the Nitrosospira-affiliated bacteria. Although the diversities of the ammonia oxidizers appear to be similar for the two sites, only half of the restriction patterns are common to both sites, which could be explained by the differences in ammonium concentrations, which are much lower in the upper estuary than in the river at the effluent outlet. These results imply a significant immigration and/or selection of the ammonia-oxidizing bacterial population along the continuum of the Seine River from Paris to the estuary.