Nearly 6 m of uncompacted muddy sediment was recovered from the floor of the northern Coorong Lagoon in the core Coorong #5. Radiocarbon analyses of molluscan shells indicate that sedimentation at the core site commenced before 6830 ± 90 yr cal BP, and the presence of Pinus pollen confirms a modern age for the uppermost 0.5 m. Microfossils extracted from the core sediment samples, 2 cm slices at 10 cm intervals, included the foraminifera Ammonia sp., Elphidium excavatum and Elphidium gunteri; the ostracods Osticythere baragwanathi and Leptocythere lacustris; and charophyte oogonia. Shell fragments of the estuarine bivalve Spisula (Notospisula) trigonella in the lowermost 0.7 m of the core are evidence that these sediments were subject to some marine influence, but the absence of foraminifera and ostracods from this same interval indicates that at the core site salinity was not sufficient to support populations of these organisms. Thus, prior to 6830 ± 90 yr cal BP the Younghusband Peninsula was in place, in part isolating the northern lagoon from the Southern Ocean. The initial recorded salinity event is signified by abundant Ammonia sp. at a core depth of 5.2 m. The duration of this event was relatively brief; foraminifera were mostly absent in the immediately overlying 2 m, representing ca 700 yr of sedimentation. This observation is attributed to substantial inflow of freshwater from the River Murray. In the upper 3.0 m, Ammonia sp. was present in most core samples indicating that for most of the past 6000 years the Coorong Lagoon has been sufficiently saline to support a continuing population of this species. At a core depth of 1.3 m, the sediment sample yielded >2000 tests of Ammonia sp., and they were accompanied by maximum pre-modern numbers of E. excavatum, O. baragwanathi and oogonia. Taken together, these data signify the maximum pre-modern salinity event recorded in the core sediments, probably correlating in time with regional drought conditions at ca 3500 yr BP. Elphidium gunteri is confined to the modern sediments where it is abundant and accompanied by equally large numbers of Ammonia sp., E. excavatum, O. baragwanathi and L. lacustris. These data collectively indicate water conditions that are significantly changed from those that prevailed in the Coorong Lagoon for most of the Holocene.