Abstract October–September runoff increased 6% and 17% in the upper (UMRB) and lower (LMRB) Missouri River basins, respectively, in a recent (1990–2019) climate in comparison with a past (1960–89) climate. The runoff increases were unanticipated, given various projections for semipermanent drought and/or aridification in the North American Great Plains. Here, five transient coupled climate model ensembles are used to diagnose the effects of natural internal variability and anthropogenic climate change on the observed runoff increases and to project UMRB and LMRB runoff to the mid-twenty-first century. The runoff increases observed in the recent climate in comparison with the past climate were not due to anthropogenic climate change but rather resulted mostly from an extreme occurrence of internal multidecadal variability. High runoff resulted from large, mostly internally generated, precipitation increases (6% in the UMRB and 5% in the LMRB) that exceeded simulated increases attributable to climate change forcing alone (0%–2% intermodel range). The precipitation elasticity of runoff, which relates runoff sensitivity to precipitation differences in the recent climate in comparison with the past climate, led to one–threefold and two–fourfold amplifications of runoff versus precipitation in the UMRB and LMRB, respectively. Without the observed precipitation increases in the recent climate in comparison with the past climate, effects of human-induced warming of about 1°C would alone have most likely induced runoff declines of 7% and 13% in the UMRB and LMRB, respectively. Ensemble model simulations overwhelmingly project lower UMRB and LRMB runoff by 2050 when compared with 1990–2019, a change found to be insensitive to whether individual realizations experienced high flows in the recent climate. Significance Statement Declines in Missouri River basin runoff under climate change pose serious threats to communities that depend on riverine transport, irrigated agriculture, and aquatic recreation. Concerns arising from reports and projections of semipermanent drought in the basin have yet to be realized; observed runoff was greater in a recent climate (1990–2019) than in a past climate (1960–89). We found that the observed runoff increase from past to recent climates was due not to anthropogenic influences but rather to internal multidecadal variability that led to unlikely precipitation increases (<10% probability) that overwhelmed the drying effect of warming temperatures. Model simulations indicate that a modest reduction in runoff of ∼7%–15% was most likely from the past climate to the recent climate.
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