In Australia, there is a scarcity of high resolution hyrdoclimate reconstructions for the last several millennia. Fluvial-marine sediments offer a potential avenue for examining trends in freshwater input to coastal settings and, by inference, past hydroclimates. Here, major elemental geochemistry, δ13C and C:N ratios of organic matter, grain size and diatom species abundance, measured in a 4.4 m long sediment core collected from Moreton Bay, in east coast Australia, are used to infer the relative freshwater discharge of the adjacent catchment over the last ~1500 years. Reduced freshwater discharge into the Bay occurred from 630 to 1200 CE, especially between 1100 and 1200 CE. A broad increase in discharge is indicated after 1300 CE, extending to the present. The initial shift to the prolonged wet period coincides with both a decrease in the frequency of ‘dry’ El Niño events based on regional records from the austral Pacific, and a broad hemispheric-scale cooling trend. This record provides further insight into low amplitude climate variability in the Australian subtropics over the last 1000 years, supporting efforts in both forecasting current and future climates, and managing regional water resources. Importantly, instrumental records do not cover the full range of natural climate variability experienced in the region over the last 1000 years.