The feeding habits of Padogobius bonelli (Bonaparte, 1846) were studied in two sites in the Orba stream (NW Italy), characterised by natural or altered flow conditions. The species fed mainly on aquatic insects, positively selecting Chironomidae, Simuliidae, Hydroptilidae and negatively Baetidae and other taxa. We hypothesised that size, mobility and handling time were on the basis of the detected feeding preferences, more than prey abundance in the substratum. When studying the variation of the diet with size, we detected that trophic spectrum of the species increases with fish dimensions. Comparing the populations of the two sites, we detected some interesting differences: fish from the natural flow site were generally larger and presented a broader trophic spectrum than fish from the altered flow site. Our study supports the hypothesis that fluctuating water levels may have evident impacts at different biotic scales, from biodiversity reductions to diet alterations.