Distribution of benthic invertebrates is determined by number of variables, such as current velocity, mineral substratum size, macrophytes, biotic interactions and the amount and quality of organic matter. Even in a small part of a stream it is possible to find habitats with very different conditions. These habitats are so different that each of them is inhabited by its own special species communities. In this study a few habitats have been sampled in a short part (about 100 m) of the small brook differing in structure of substrate and amount of organic matter: sandy bottom, fine sediment from place with zero current velocity, accumulated coarse woody debris and gravel with different contains of leaf litter. All substratum have been taken from the area of 0.05 m2 and depth of approximately 5 cm. Each sample has been analyzed in a laboratory and characterized by the amount of FPOM, coarse woody debris, leaf litter and grain particle size. Affinity of benthic invertebrates to substrate is discussed and each habitat is characterized by its specific species aggregation.