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The South American summer monsoon (SASM) profoundly influences tropical South America’s climate, yet understanding its low-frequency variability has been challenging. Climate models and oxygen isotope data have been used to examine the SASM variability over the last millennium (LM) but have, at times, provided conflicting findings, especially regarding its mean-state change from the Medieval Climate Anomaly to the Little Ice Age. Here, we use a paleoclimate data assimilation (DA) method, combining model results and δ¹⁸O observations, to produce a δ¹⁸O-enabled, dynamically coherent, and spatiotemporally complete austral summer hydroclimate reconstruction over the LM for tropical South America at 5-year resolution. This reconstruction aligns with independent hydroclimate and δ¹⁸O records withheld from the DA, revealing a centennial-scale SASM intensification during the MCA-LIA transition period, associated with the southward shift of the Atlantic Intertropical Convergence Zone and the strengthening Pacific Walker circulation (PWC). This highlights the necessity of accurately representing the PWC in climate models to predict future SASM changes.