A microcosm experiment was designed to evaluate the effects of the simulated deposition of uncontaminated dredged material on nematode assemblages from estuarine intertidal mud. The main objective was to assess the ability of nematodes to migrate vertically into native muddy and non-native sandy sediment deposited in different amounts and frequencies. Results from univariate and graphical methods of data-evaluation revealed that nematodes were capable of migrating over a wide depth range from the bottom mud layer into the top layer of deposited sand and mud. A diverse mud assemblage of nematodes was able to survive in non-native fine sand for the experimental period of 2 mo. Multivariate analyses showed that the amount of deposit and the frequency of deposition were interactive factors. A high amount of sediment deposited once at the beginning of the experiment caused more severe changes in assemblage structure than the same amount deposited in more frequent but smaller doses. The response of most species to the experimental treatments appeared to be an integrated response to the enhancing effect of food input accompanying the deposit and the negative effect of burial. Upward migration of nematodes is a process which has often been underestimated in its importance for recolonisation of areas where uncontaminated dredged material is deposited. Active migration of nematodes can significantly affect the recovery of a dredgings disposal site.