We assessed the response of soil fauna to natural environmental gradients triggered by different dynamics of hydrological conditions. Four sites differing in the dynamics of groundwater-surface water interactions, type of soil and type of wetland vegetation were selected along a transect running from a river channel to the margin of the valley in the floodplain. Soil macrofauna, represented by millipedes, terrestrial isopods and earthworms, and soil mesofauna (collembolans) were investigated along that transect. Our results demonstrate that soil macrofauna and mesofauna variability differ across examined peatforming wetlands. The effect of hydrological conditions associated with flooding emerged as a significant predictor of the variability in soil macrofauna with regard to millipedes and terrestrial isopods, but not earthworms. We concluded that the interactive processes reflected in the landscape mosaic, complex spatiotemporal environmental gradients and biogeochemical factors determine the distribution of soil macro and mesofauna within peat-filled river floodplains, although soil fauna components differ in the response across the examined sites.