Within a subtropical estuary in southern Brazil, an experiment was carried out to test the hypotheses that the deposit feeding macrofaunal polychaete Laeonereis acuta affects nematode community structure and the vertical distribution patterns of nematodes in sediments. Inclusion cages were deployed with two different densities of the polychaete and meiofaunal nematodes were sampled from six different vertical sediment layers: 0–1, 1–2, 2–4, 4–6, 6–8 and 8–10 cm depth. Although L. acuta did change the vertical distribution of both nematode and trophic groups in the sediment, allowing nematodes to inhabit deeper sediment layers, there were no apparent effects of different polychaete densities.