The nematode communities of four different micro-habitats in an unpolluted first-order stream were investigated over a 13-month period in a study of the sediment and the biofilms on dead wood, macrophytes and leaf litter. Nematode abundances, biomass and secondary production were analysed, together with the species composition, proportion of feeding types and diversity of the nematode communities of the micro-habitats. Differences between the investigated micro-habitats in terms of seasonal variations, species composition, proportion of feeding types and diversity were expected. The annual mean values of nematode abundance, biomass and secondary production differed significantly between the micro-habitats. Abundances were highest on dead wood, whereas biomass and secondary production were highest in sediment. In the sediment and on leaf litter, nematode abundance and biomass showed pronounced seasonal patterns. The largest contribution to the total secondary production of the stream was from sediment nematodes. In total, 108 nematode species were detected in the micro-habitats during the 13-month study. Comparisons between them revealed differences in nematode species composition. The annual mean species number was significantly higher in sediment and on leaf litter than on dead wood and macrophytes, whereas the annual mean Shannon-Wiener index was significantly higher in sediment than at all other micro-habitats. All micro-habitats in the studied stream, as well as the stream as a whole, were dominated by nematode species belonging to the deposit feeders. Our study clearly showed that the composition of nematode communities from different micro-habitats within a single stream reach can differ markedly.