Sediment samples have been examined from 51 locations between the Narrows Bridge and Fremantle Harbour in the Swan River estuary. All have yielded foraminifera and all but one provided data in which distinctive trends can be recognized.

Foraminiferal number (number of specimens in 10 g dry weight of sample) decreases upstream until near Narrows Bridge, where it increases again. Values are >2500 for most samples through Fremantle Harbour to Blackwall Reach and just past Point Walter. The higher numbers correlate with the outside of the bends in the river, reflecting a higher energy, more marine influence. The highest value is ~10,000 at Station 2. Values of 500–2500 occur in the inside of the river bends between Fremantle and Blackwall Reach, probably correlating with a slightly lower energy environment. There is a separate region of 500–2500 values in a narrow strip from the Narrows Bridge into Melville Water, probably due to the influx of river-borne nutrients; the composition of faunas contributing to this high value is quite different from that between Fremantle and Blackwall Reach. Two regions of lower values (100–500 and <100) are recognizable, both confined to Melville Water, the lower values apparently coinciding with the mud-filled basin of the river. In the Fremantle Harbour - Blackwall Reach section of the river, Ammonia cf. aoteana (Finlay) makes up <5% of the foraminiferal fauna, but >50% of faunas near the Narrows Bridge and in most of Melville Water, excluding the shallower parts particularly to the northwest. In contrast to A. cf. aoteana, miliolids make up >50% of faunas in the southern side of Blackwall Reach and extend just into Melville Water. They make up <5% of the fauna where A. cf. aoteana is >50%. The inverse relationship between A. cf. aoteana and miliolids is very marked. Elphidium constitutes up to 90% of the foraminiferal fauna, but this polyspecific estuarine genus is concentrated towards the marine end of the estuary. Diversity in foraminifera decreases and dominance increases upstream.

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