The impact of removing riparian vegetation, channel straightening, and fluctuations in flow regime on trophic structure, reproductive success, and growth rate of fishes was assessed in a natural (Jordan Creek(JC)) and modified (Big Ditch(BD)) headwater stream in eastcentral Illinois. Fish in JC were predominantly benthic insectivores and insectivore - piscivores: trophic structure, age structure, and biomass were stable between years and seasons. Adult fish and recruits in BD were predominantly generalized insectivores, omnivores, and herbivore-detritivores; the last two were primarily mid-river species (Carpoides cyprinus and Dorosoma cepedianum). Considerable seasonal and annual variation in trophic structure, total biomass, and age structure occurred in BD associated with annual fluctuations in flow regime, abundance of organic substrates, and reproductive success of mid-river species.