The aim of the study was to estimate the effect of habitat factors such as moisture conditions and some physicochemical soil characteristics on the structure of the vegetation and the soil seed bank, and to compare species composition of the vegetation cover and the seed bank along the soil moisture and fertility gradients in closed depression in agricultural landscape. Based on the averaged results of the extent and time of stagnation of the water, along the transect four habitat moisture zones were distinguished (dry, periodically moist, moist, and wet). In eighteen study plots we analysed flora, soil seed bank, and contents of Ca, Mg, K, Mn, Fe and pH of the soil. The analysed closed depression is characterised by high variability in moisture conditions and in the physical and chemical properties of the soil. The most important factors affecting the diversity of the vegetation cover and seed bank were the duration of water stagnation and the content of Fe and Mn in the soil. The lowest plant species richness and the smallest seed resources were determined for the wet zone of the depression. An increase in the habitat moisture level was accompanied by a decline in the floristic similarity between the vegetation cover and the seed bank.