Sources of variability such as sampling method, sample preparation, and sample analysis (taxonomy) might affect our ability to measure differences in community structure between sites in environmental effects studies. It is therefore important to ensure that changes in community structure related to the physical or chemical differences between sites are not hidden by other sources of variability within a site. The goal of this study was to quantify the amount of variability in benthic diatom community structure related to sampling and laboratory procedures. Our results showed that variability in community structure was minimal among replicate microscope slides (<1%) and among samples collected within a site (1.8%). Variability in community structure was substantially higher between sites located in one stream (16.6%), and highest across streams (59.6%). This suggests that field sampling and laboratory methods do not contribute a large amount of variation into our analyses of benthic diatom community structure across sites. © Springer 2005.