Fish and lampreys were sampled by electrofishing in the Pilica River tributaries (the Vistula catchment, Poland) in 1992–1994 and 2003–2005. The patterns in fish assemblages were recognized on the basis of fish biomass using Kohonen's self-organizing map (SOM) technique, combined with the indicator values (IndVal) for assessment of associations of fish species with particular SOM regions (and respective environmental conditions). Although the fish samples were clustered mostly according to the stream features (size, regulation, and pollution), a weaker temporal gradient indicated a recovery of the ichthyofauna in some smaller streams. The larger tributaries served as sources of colonisers for both the Pilica and the smaller streams. The differences between SOM subclusters in the quality of the aquatic environment were effectively presented with certain biological measures, including the dominances of potentially large species and non-psammophilous rheophils, which are proposed as good bioindicators. It is worth mentioning that some closely related species (ide and dace, silver bream and bream, golden loach and spined loach, and Ukrainian lamprey and brook lamprey) were significantly associated with different SOM regions (and respective environmental conditions), perhaps in this way avoiding competition. Copyright © 2013 John Wiley & Sons, Ltd.