The Czarny Dunajec River, Polish Carpathians, has been considerably modified by channelization and gravel mining-induced channel incision and it varies in morphology from a single-thread, incised or regulated channel to an unmanaged, multi-thread channel. For twelve cross-sections with between 1 and 4 flow threads, the abundance and diversity of fish fauna were determined by electrofishing and compared with an assessment of hydromorphological river quality and the variation in flow depth, velocity and bed material size. Hydromorphological quality of the river varied between high-status conditions (Class 1) in unmanaged, multi-thread cross-sections with varying proportions of islands and Class 4 in channelized cross-sections. The increased number of low-flow channels in a cross-section was associated with a larger aggregated width of low-flow channels and greater variation in flow depth, velocity and bed material size. Single-thread cross-sections hosted only 2 fish species and 13 individuals on average, whereas 3-4 species and 82 individuals on average were recorded in cross-sections with four low-flow channels. Regression analysis indicated that both the number of fish species and individuals increased linearly with increasing variation in depth within a cross-section and exponentially with improving hydromorphological river quality, while they were unrelated to flow width, suggesting that it is the increase in variability of habitat conditions rather than simple habitat enlargement, that supported the increased abundance and diversity of fish fauna in the multi-thread cross-sections. This study shows that the simplification of flow pattern and the resultant degradation of hydromorphological river quality, caused by human impacts, is reflected in remarkable impoverishment of fish communities and that recovery of these communities will require an increase in morphological complexity of the river. Figure 3. Scores given by four evaluators for the hydromorphological river quality in the investigated cross-sections of the Czarny Dunajec and the average of the four estimates. The number of flow threads in each cross-section is also indicated Figure 5. Scatter plots of physical characteristics of the Czarny Dunajec versus the number of flow threads in the investigated cross-sections.The significance of the difference of the parameter means between the cross-sections with one and four low-flow channels were determined by Mann-Whitney test. The dashed lines link the parameter means between the two groups of cross-sections