Bottom-feeding fish can exert strong top-down pressure on benthic invertebrates while also causing mechanical disturbance of the sediment. In our laboratory study, we investigated the influence of predation and disturbance-induced water column emigration on meiofauna, triggered by the armored catfish Corydoras aeneus. We hypothesized that both factors would significantly reduce the abundance of meiofauna, depending on their body size. Accordingly, we also expected a change in the nematode community structure. After 24 h, the abundances of nematodes, tardigrades, hydracarina, copepods and oligochaetes were significantly lower than in control aquariums without fish, in the latter two groups primarily due to predation. All other taxa were equally affected by predation and emigration. Within the nematodes, mainly large individuals (≥ 1 mm) were consumed, while smaller worms (< 1 mm) were increasingly dispersed. This, though it did not reduce species numbers, resulted in altered size and species composition. Our results show that the real top-down effects can quickly be overestimated as emigration of prey is overlooked and, on the other hand, that fish may also influence adjacent, undisturbed areas due to subsequent immigration of meiofauna.