Enhanced delivery of sediment and nutrients to the Great Barrier Reef has the potential to profoundly influence ecological processes in this natural icon. Within the Fitzroy River Basin (FRB) of north-eastern Australia, natural impoundments such as Crescent Lagoon provide an invaluable archive of accumulated sediment that can be dated using multiple techniques to reconstruct the history of sediment export. During the last century, net rates of accumulation of sediment remain similar; however, large variations in sediment sources are apparent. A major sedimentary and geochemical discontinuity is present between ~45 to 29 years before present. Within this time interval a redox front is preserved corresponding to a change in organic matter influx; C3 plant detritus derived from the onset of broadscale agriculture within the FRB provided an assimilable carbon source resulting in more reducing conditions within the sediments. Statistical correlations demonstrate a notable correspondence between some sediment fractions supporting the notion of a short-lived disturbance to the sedimentation regime in the 1960–70s.