We examined whether small omnivorous fishes (smaller than ,100 mm long) integrate littoral, pelagic and benthic pathways in a shallow, eutrophic lake (Lake Izunuma, Japan). The surface of the lake was covered by a dense vegetation of floating-leaved macrophytes, and small species dominated the icthyofauna. We determined the d 13 C and d 15 N ratios of five dominant species of small omnivorous fishes. Using a stable isotope analysis in the R mixing model, we determined the possible contribution of three potential food sources (epiphytic algae, zooplankton and zoobenthos (larval chironomids)) to omnivorous fish tissue compositions. Four omnivorous fishes (Gnathopogon elongatus elongatus, Pseudorasbora parva, Biwia zezera and Tridentiger obscurus) subsisted largely on epiphytic algae and zooplankton, whereas zoobenthos contributed little to their diets. Acheilognathus rhombeus subsisted mostly on epiphytic algae. Thus, in this shallow, eutrophic lake, omnivorous fishes incorporated both littoral and pelagic production into the food web, but rarely benthic production. The dominant benthic chironomid larvae often burrow several centimetres into the sediment, and the low dietary contribution of zoobenthos to small fishes may be due to inefficiency at foraging on buried benthos associated with fish body size.Additional keywords: chironomid, cyprinid, d 13 C and d 15 N, isotope mixing model, methane-oxidising bacteria.