The structure of phytobenthic diatom communities was studied to reveal differences between natural and channelized river sections in Slovenia. As part of the national monitoring of surface waters, samples of phytobenthos were collected at 85 sites throughout the country according to standard protocols. At the same time, basic environmental parameters were also assessed. Trophic (TI) and saprobic (SI) indices were calculated based on diatoms and other algae, while diversity indices and gradient analyses were performed only for the diatom community. The results showed that channelized rivers harbor significantly more diverse benthic diatom communities than natural sections, mainly due to the significantly higher number of motile diatom taxa that are able to take advantage of more nutrient-rich and less-shaded river sections because of their high adaptability. Selected environmental parameters explained 34% of the variability in diatom community structure when taxa were classified into ecological types. The removal ofAchnanthidium minutissimumyielded clearer results (24.1%) than the total species matrix (22.6%). Therefore, we suggest excluding this taxon from calculations of TI, SI, or other indices when it is determined asA. minutissimumcomplex, becauseA. minutissimumcomplex was most abundant in both types of reaches in our study and has a wide ecological amplitude, which reduces the indicative power of the diatom community in the evaluation of environmental conditions and ecological status.