Chironomid retreats, constructed out of sand grains upon submerged wood debris, increase the surface area available for diatom colonization. The three dimensional substratum afforded by chironomid tubes supports up to twelve times the diatom biovolume found upon adjacent, unmodified substratum in a northern Michigan stream. Diatom enumeration within scrapings from small defined areas on artificial substrata, combined with examination of intact natural substrata through scanning electron microscopy (SEM), reveals distinct microdistribution patterns. The larval retreats of two major taxa of tube-dwelling chironomids (Micropsectra sp. and Pseudodiamesa cf. pertinax Garrett) display significantly different diatom communites relative to adjacent masonite substratum. Substratum without chironomid tubes is primarily colonized by Achnanthes minutissima Kutz. and Cocconeis placentula Ehr., exhibiting the lowest species diversity of microhabitats examined. The diatom flora upon sand tubes of Micropsectra sp. is dominated by Opephora martyi Herib., as is the flora of sand grains collected from the stream sediment load. These two microhabitats exhibit a high community similarity (SIMI). The SIMI index also suggests that the flora of P. pertinax tubes is highly similar to that of sand grains. Diversity, however, is almost three times greater on P. pertinax tubes and SEM observations reveal that this microhabitat is characterized by a more spatially complex flora; Nitzschia and Navicula spp. dominate the upperstory, and O. martyi is located on underlying sand grains. Results indicate that tube-building chironomids in Carp Creek affect diatom microdistribution by: (1) stabilizing sand grains and associated flora within their retreats, (2) providing a ’refugium’ for upperstory diatom taxa from the mayfly grazer, Baetis vagans McDunnough (Insecta: Ephemeroptera), and (3) through local nutrient enrichment.