Summer monsoon rainfall in northeastern (NE) Australia exhibits substantial interannual variability resulting in highly variable river flows. The occurrence and magnitude of these seasonal river flows are reliably recorded in modern inshore corals as luminescent lines. Here we present reconstructed annual river flows for two ~120 year mid-Holocene windows based on luminescence measurements from five cores obtained from three separate coral colonies. We were able to cross-date the luminescence signatures in four cores from two of the colonies, providing confidence in the derived reconstruction. Present-day NE Australian rainfall and river flow are sensitive to El Niño–Southern Oscillation (ENSO) variability, with La Niña (El Niño) events typically associated with wetter (drier) monsoon seasons. Thus, our replicated and annually resolved coral records provide valuable insights into the northern Australian summer monsoon and ENSO variability at a key period (6 ka) when greenhouse gas levels and ice sheet cover were comparable to the preindustrial period but orbital forcing was different. Average modern and mid-Holocene growth characteristics were very similar, suggesting that sea surface temperatures off NE Australia at 6 kyr were also close to present values. The reconstructed river flow record suggests, however, that the mid-Holocene Australian summer monsoon was weaker, less variable from year to year (possibly indicative of reduced ENSO variability), and characterized by more within-season flood pulses than present. In contrast to today, the delivery of moisture appears to have been dominated by eastward propagating convective coupled waves associated with the Madden-Julian Oscillation.