Freshwater ecosystems are subject to many anthropogenic threats. Understanding aquatic community responses and identifying mitigation actions to these threats is a major challenge for ecologists and natural resource managers. Here, we investigated fish community responses along a gradient of anthropogenic impacts in the Atlantic Forest ecoregion of southeastern Brazil. We analyzed fish stomach contents and assessed the response of five food web metrics to variation in land use change at different scales. We also evaluated four metrics for intra-guild comparisons in omnivore, insectivore and algivore-insectivore guilds. Food web specialization decreased in streams with higher nutrient input and low canopy cover, suggesting greater resource sharing by these fish communities. Fish from the algivore-insectivore guild consumed fewer types of aquatic insects in deforested streams. However, the opposite pattern was observed within the insectivore guild with individuals consuming a greater variety of prey in deforested streams. Deforestation, and increases in water temperature and nutrient input influenced interspecies and intra-guild trophic relationships in fish communities, although fish community richness and intra-guild species composition remained unchanged. Our study showed that trophic interactions assessments can detect effects of land use changes on fish communities that may not be evident from measures of species richness and composition. Some food web metrics are sensitive to the direct and indirect effects of disturbance on fish communities. This approach provides information about the functional integrity of fish communities and should be considered for monitoring programs designed to protect and restore freshwater ecosystems.