Predation may significantly control number and density of coexisting species. The effects of predation on species diversity have traditionally been tested in experiments and theoretical models of simple trophic systems. In complex natural ecosystems, however, disentangling multiple sources of variation is difficult. In groundwater-fed environments, a significant effect of predation can be expected due to the relatively stable environmental conditions; however, it has never been properly examined. We analysed species diversity and total abundance of macroinvertebrate assemblages in 48 Western Carpathian spring fens, separately for whole sites and mesohabitat/season, and partitioned the effects of predation intensity from those of environmental variables in robust models using a bootstrapping technique. We verified our results by accounting for taxa resistant to predation. The assumption that predation-mediated coexistence of species is the main mechanism responsible for the relatively species-rich assemblages in the Western Carpathian spring fens was not supported. However, predation may significantly influence abundance of non-predatory species and, under some conditions, it may contribute to explaining patterns in species diversity. The effect of predation did not differ between the mesohabitats with different stability. However, we found higher environmental control in spring and a stronger effect of predators in autumn, which suggests that different mechanisms influence fen assemblages in different seasons. Our study provides a new robust approach how to test the effect of predation on natural macroinvertebrate assemblages. The importance of predation was lower than expected in equilibrium assemblages but it may vary in time.