Increases in food production are imposing new and greater stressors on global ecosystems, but effects on food web structure remain poorly studied. We tested whether the food web energy pathways and trophic structure of fish communities were altered by aspects of agriculture, including land cover changes, riparian habitat and water quality. A generalist predator (Semotilus atromaculatus) was analysed using stable isotopes to quantify terrestrial and aquatic resource use and trophic structure. Our results show aquatic energy input increases and trophic position decreases significantly with increased agricultural impact and nutrients. We show that asymmetric restructuring exists in impacted systems since generalists are unable to link aquatic and terrestrial energy pathways in riparian systems and may reduce the resilience of the system, although this may be mitigated by local refuge riparian habitat. We suggest future actions to determine the size of riparian buffer needed to mitigate the effects of agricultural land use.