The stream habitats are formed by processes originating at various spatial scales. We analyzed the structure of oligochaete communities and its relationships to characteristics of catchment, floodplain, channel morphology and water chemistry. Substrate type is important component of habitat characteristics affecting oligochaetes distribution. The AQEM multihabitat sampling method was used for collecting macroinvertebrate samples at 24 sites representing gradient of organic pollution (14 sites) and morphological degradation (10 sites). All sites are small streams situated at altitude between 200 and 500 m a.s.l., with catchment area ranging from 10 to 50 square km. Biological material was collected during three periods - summer and autumn 2002 and spring 2003. Site characteristics were obtained partly from field investigation and partly from maps and GIS sources. The landuse, runoff types, geology and slope were evaluated at catchment scale. Landuse in the floodplain, riparian zone features and hydromorphological field survey (River Habitat Survey) represented factors recorded at the scale of river stretch. Taxonomic composition of aquatic oligochaetes and their functional role within macroinvertebrate communities were analyzed. The environmental parameters related to oligochaete community structure at studied sites were identified using multivariate statistics. The effect of season was evaluated.