Selection on naturally-occurring hybrid individuals is a key component of speciation theory, but few studies examine the functional basis of hybrid performance. We examine the functional consequences of hybridization in nature using the freshwater sunfishes (Centrarchidae), where natural hybrids have been studied for over a century and a half. We examined bluegill (Lepomis macrochirus), green sunfish (Lepomis cyanellus), and their naturally-occurring hybrid using prey capture kinematics and morphology to parameterize suction feeding simulations on divergent parental resources. Hybrid individuals exhibited intermediate kinematics between the two parental species. However, performance assays indicated that hybrids display performance most similar to the worse-performing species for a given parental resource. Our results show that intermediate hybrid phenotypes can be impaired by a less than intermediate performance and hence suffer a larger loss in fitness than could be inferred from morphology alone.