AbstractRock rip‐rap is commonly used by river engineers for bank stabilization. However, there is a general lack of information on invertebrate communities inhabiting these structures. This study examines the permanent and temporary meiofauna dwelling in dense clumps of an aquatic moss Fontinalis antipyretica growing on rock rip‐rap along a side channel of the Morava river, Czech Republic. We estimated the amount of fine particulate matter (total trapped matter, TM) trapped in the moss as both a habitat and food source for meiofauna. Total mean numbers of the moss‐dwelling meiofauna per 10 g dry weight of moss and 1 m2 of the bottom area were 253 917 ± 178 335 (mean ± SD) and 7 160 461 ± 5 029 047 individuals, respectively, during October 1999–November 2000. Out of 20 operational taxonomic units, Bdelloidea was the dominant group with about 76% of the total meiofauna numbers followed by Monogononta (11.23%), Nematoda (6.38%), Chironomidae (4.08%) and Oligochaeta (1.06%). Coarse trapped matter (500–1000 µm) contributed about 4% to the total, medium TM (100–500 µm) around 14% and the finest TM (30–100 µm) 82%. Organic matter (OM) forms 10% of the total TM. The seasonal variations in TM, OM and mineral matter and their size fractions have significantly correlated (Spearman rank correlation coefficient, P < 0.05 or 0.01) with densities of Oligochaeta, Hydrachnidia, Cladocera, Harpacticoida, nauplii of Copepoda, Chironomidae. In regulated channels, rock rip‐rap overgrown by aquatic bryophytes is desirable because it increases the spatial diversity of habitats and supports considerably higher numbers of meiofauna compared to the gravel bed and may substantially contribute to the stream metabolism. Copyright © 2002 John Wiley & Sons, Ltd.