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The Mississippi River basin drains nearly one-half of the contiguous United States, and its rivers serve as economic corridors that facilitate trade and transportation. Flooding remains a perennial hazard on the major tributaries of the Mississippi River basin, and reducing the economic and humanitarian consequences of these events depends on improving their seasonal predictability. Here, we use climate reanalysis and river gauge data to document the evolution of floods on the Missouri and Ohio Rivers—the two largest tributaries of the Mississippi River—and how they are influenced by major modes of climate variability centered in the Pacific and Atlantic Oceans. We show that the largest floods on these tributaries are preceded by the advection and convergence of moisture from the Gulf of Mexico following distinct atmospheric mechanisms, where Missouri River floods are associated with heavy spring and summer precipitation events delivered by the Great Plains low-level jet, whereas Ohio River floods are associated with frontal precipitation events in winter when the North Atlantic subtropical high is anomalously strong. Further, we demonstrate that the El Niño–Southern Oscillation can serve as a precursor for floods on these rivers by mediating antecedent soil moisture, with Missouri River floods often preceded by a warm eastern tropical Pacific (El Niño) and Ohio River floods often preceded by a cool eastern tropical Pacific (La Niña) in the months leading up peak discharge. We also use recent floods in 2019 and 2021 to demonstrate how linking flood hazard to sea surface temperature anomalies holds potential to improve seasonal predictability of hydrologic extremes on these rivers.

Changes in climate are expected to influence discharge of the lower Mississippi River, but projections disagree on whether discharge will increase or decrease over the coming century. Using a reconstructed median peak annual flow for the past 1,500 years based on geomorphic scaling laws, we show that discharge on the lower Mississippi River decreased during the Medieval era (c. 1000–1200 CE)—a period of regionally warm and dry conditions that serves as a partial analog for projected warming. These changes in discharge inferred from channel morphology track discharge simulated in the Community Earth System Model Last Millennium Ensemble. Simulations show that decreased Medieval era discharge is driven primarily by regionally enhanced evapotranspiration. Our findings are consistent with 21st century projections of decreased discharge on the lower Mississippi River under moderate greenhouse forcing scenarios, and demonstrate consistency between reconstructed and simulated discharge over the last millennium.

Floods and droughts in the Mississippi River basin are perennial hazards that cause severe economic disruption. Here we develop and analyze a new lipid biomarker record from Horseshoe Lake (Illinois, USA) to evaluate the climatic conditions associated with hydroclimatic extremes that occurred in this region over the last 1,800 years. We present geochemical proxy evidence of temperature and moisture variability using branched glycerol dialkyl glycerol tetraethers (brGDGTs) and plant leaf wax hydrogen isotopic composition (δ²H_wax) and use isotope‐enabled coupled model simulations to diagnose the controls on these proxies. Our data show pronounced warming during the Medieval era (CE 1000–1,600) that corresponds to midcontinental megadroughts. Severe floods on the upper Mississippi River basin also occurred during the Medieval era and correspond to periods of enhanced warm‐season moisture. Our findings imply that projected increases in temperature and warm‐season precipitation could enhance both drought and flood hazards in this economically vital region.