The Yarqon is a slow-flowing Mediterranean stream with three ecologically distinct sections, with varying abiotic conditions and anthropogenic influences. We used the Yarqon as a test habitat to study the effect of flow on microbial communities. Stream water samples from three distinct abiotic conditions: "clean", "human-impacted" and "brackish" sections were incubated in situ in dialysis bags at each of these sections for approximately 73 h. The samples were retrieved and analyzed by ARISA (automated ribosomal internal spacer analysis) and viable counts. Diversity estimates showed that free-living assemblages from the middle human-impacted section increased in diversity, while assemblages from the upper-clean section decreased in diversity unless planted in their site of origin. Samples originating from the brackish western section decreased in diversity wherever they were incubated. The ARISA profiles of the samples usually grouped by origin rather than by incubation location, implying that the rate of change of the free-living bacterial assemblages due to the shift in environment is relatively slow. Nevertheless, introducing free-living bacteria from the human-impacted section into the freshwater section resulted in a profile more similar to the latter, indicating a profound niche influence on these microbial assemblages. Copyright © 2012 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.