River profiles are shaped by climatic and tectonic history, lithology, and internal feedbacks between flow hydraulics, sediment transport and erosion. In steep channels, waterfalls may self-form without changes in external forcing (i.e., autogenic formation) and erode at rates faster or slower than an equivalent channel without waterfalls. We use a 1-D numerical model to investigate how self-formed waterfalls alter the morphology of bedrock river longitudinal profiles. We modify the standard stream power model to include a slope threshold above which waterfalls spontaneously form and a rate constant allowing waterfalls to erode faster or slower than other fluvial processes. Using this model, we explore how waterfall formation alters both steady state and transient longitudinal profile forms. Our model predicts that fast waterfalls create km-scale reaches in a dynamic equilibrium with channel slope held approximately constant at the threshold slope for waterfall formation, while slow waterfalls can create local channel slope maxima at the location of slow waterfall development. Furthermore, slow waterfall profiles integrate past base level histories, leading to multiple possible profile forms, even at steady-state. Consistency between our model predictions and field observations of waterfall-rich rivers in the Kings and Kaweah drainages in the southern Sierra Nevada, California, supports the hypothesis that waterfall formation can modulate river profiles in nature. Our findings may help identify how bedrock channels are influenced by waterfall erosion and aid in distinguishing between signatures of external and internal perturbations, thereby strengthening our ability to interpret past climate and tectonic changes from river longitudinal profiles.