A paradoxical situation was found in the sand filters of a cold marine mesocosm: meiofaunal masses which were large enough to inhibit the mineralization and nitrification processes coexisted with nitrogen cycling bacteria. To test whether the copepod-dominated meiofauna were resident and actively feeding or transient and carried passively through the sand filters, residence times (RTs) were measured for various meiofaunal groups in a newly started filter and in a long established one. Most meiofauna colonized the newly started filter in less than 6 h, but their RTs were less than 24 h. In contrast, RTs were 147 d for halacarids, 291 d for harpacticoid copepods and 1228 d for nematodes in the long established filter. Mesocosm periphyton, which occupied a large fraction of the mesocosm surface area and was characterized by high meiofaunal densities, was probably the main source of meiofauna in the sand filters. Pool sediments, consisting of gravel or sand, were second to periphyton and contributed hydrozoans and mesopsammic species to the filters. The small copepod Pseudonychocamptus proximus progressively replaced the large Tisbe furcata in sand filters during the fall of 1995 and was responsible for the large increase in meiofaunal biomass observed after spring 1996. This replacement was presumably facilitated by the copepod size selection process operated by the filters. Large copepods were retained by the surface layer of sand or brought up by the backwash water and then exit the mesocosm through the drain. High meiofaunal populations did not significantly affect nitrogen cycling bacteria in sand filters probably because meiofauna also fed on other abundant food sources which were carried in by the water flow.