Watershed ecology is of great importance in China because most ecological and environmental problems occur at a basin-wide scale. However, studies on watershed ecology have not yet synthesized into a unitary framework. The factors causing this dilemma in watershed ecology research are not clear; therefore, it has been difficult to precisely determine how to solve this problem. We hypothesized that this dilemma is rooted in structural defects underlying the concept of watershed ecology. By comparing the concepts of watershed ecology and riverscape, we tried to identify missing links in the formation and development of watershed ecology. The defects of watershed ecology are discussed mainly based on two original papers, "Watershed ecology (in Chinese)", published in Science & Technology Review in 1997 by Cai et al., and "Riverine landscapes: biodiversity patterns, disturbance regimes, and aquatic conservation", published in Biological Conservation in 1998 by Ward, which proposed the concepts of watershed ecology and riverine landscape, respectively. Our review showed that there have been two main defects in the conception and development of watershed ecology. First, there was no clear definition of watershed ecology when the concept was proposed, and there was no identification of core scientific questions. Second, there was no ecosystem model developed at the watershed scale to guide follow-up research on watershed ecology. We suggest defining watershed ecology as an integrative sub-discipline of ecology that is focused on solving complex eco-environmental problems at the watershed scale. A conceptual model describing the spatial heterogeneity and eco-processes of a watershed ecosystem is necessary for building a solid framework of watershed ecology.