Previous studies have shown that the impacts of climate change on the hydrologic response of the Skagit River are likely to be substantial under natural (i.e. unregulated) conditions. To assess the combined effects of changing natural flow and dam operations that determine impacts to regulated flow, a new integrated daily-time-step reservoir operations model was constructed for the Skagit River Basin. The model was used to simulate current reservoir operating policies for historical flow conditions and for projected flows for the 2040s (2030–2059) and 2080s (2070–2099). The results show that climate change is likely to cause substantial seasonal changes in both natural and regulated flow, with more flow in the winter and spring, and less in summer. Hydropower generation in the basin follows these trends, increasing (+ 19%) in the winter/ spring, and decreasing (- 29%) in the summer by the 2080s. The regulated 100-year flood is projected to increase by 23% by the 2040s and 49% by the 2080s. Peak winter sediment loading in December is projected to increase by 335% by the 2080s in response to increasing winter flows, and average annual sediment loading increases from 2.3 to 5.8 teragrams (+ 149%) per year by the 2080s. Regulated extreme low flows (7Q10) are projected to decrease by about 30% by the 2080s, but remain well above natural low flows. Both current and proposed alternative flood control operations are shown to be largely ineffective in mitigating increasing flood risks in the lower Skagit due to the distribution of flow in the basin during floods.