The basic tenet of optimal foraging theory is that animals will select habitats that provide the greatest energy return (of food resources) per unit effort spent searching to optimize their fitness. Fish living in variable environments may use specific cues that indicate optimal feeding patches relative to poorer quality patches. To examine whether carp gudgeons (Hypseleotris spp.) preferentially select habitat patches based on food resource availability, we examined their habitat use in emergent macrophyte stands (the giant rush, Juncus ingens). We tested the hypothesis that carp gudgeons selected patches based upon food availability in a floodplain billabong and experimental billabongs. Under field conditions, fine-scale associations between carp gudgeons and giant rush demonstrated patch-specific differences in their prey (chironomid) density that were positively associated with fish abundance. Furthermore, the amount of biofilm within a patch was positively associated with the density and biomass of chironomids. Experimental evidence demonstrated that carp gudgeon patch selection was independent of stem density and based upon prey density. Carp gudgeons track their food resources through time, thus maximizing their feeding returns in both natural and experimental systems.