Most large rivers in South America are fragmented by large dams, and a common management strategy to mitigate impacts has been construction of fish passes. Recent studies, however, indicate that downstream passage of adults and young fish is nil or minimal. Better understanding of this phenomenon is needed if fishways are to provide any tangible conservation value in South America. We propose, in this article, that large reservoirs impose a different kind of barrier to migrating fish: impoundments create a diffuse gradient of hydraulic/limnological conditions that affects fish behaviour and functions as an extensive environmental filter that discourages downstream movements. To develop this idea, we characterize the barriers created by dams and reservoirs by describing their distinct nature, the effects on fish migration and potential solutions. We show, for example, that dams generally prevent upstream movements, whereas reservoirs impede mainly downstream movements. In this context, we explain how fish passes, in some instances, can partially mitigate fragmentation caused by dams, but there is no technical solution to solve the barrier effect of reservoirs. In addition, we present a body of empirical evidence that supports the theory that large reservoirs are important barriers to fish migration in South America, we offer an overview of the size of reservoirs to show that impoundments typically have large dimensions, and we discuss the significance of this theory for other regions. Based on current and proposed river regulation scenarios, we conclude that conservation of Neotropical migratory fish will be much more complicated than previously believed.