The Nile basin is the second largest basin in Africa and one of the regions experiencing high climatic diversity with variability of precipitation and deteriorating water resources. As climate change is affecting most of the hydroclimatic variables across the world, this study assesses whether historical changes in river flow and sediment loads at selected gauges in the Nile basin can be attributed to climate change. An impact attribution approach is employed by constraining a process-based model with a set of factual and counterfactual climate forcing data for 69 years (1951–2019), from the impact attribution setup of the Inter-Sectoral Impact Model Intercomparison Project (ISIMIP3a). To quantify the role of climate change, we use the non-parametric Mann-Kendall test to identify trends and calculate the differences in long-term mean annual river flow and sediment load simulations between a model setup using factual and counterfactual climate forcing data. Results for selected river stations in the Lake Victoria basin show reasonable evidence of a long-term historical increase in river flows (two stations) and sediment load (one station), largely attributed to changes in climate. In contrast, within the Blue Nile and Main Nile basins, there is a slight decrease of river flows at four selected stations under factual climate, which can be attributed to climate change, but no significant changes in sediment load (one station). These findings show spatial differences in the impacts of climate change on river flows and sediment load in the study area for the historical period.