A total of 117 surface sediment samples from sites across the Pearl River Estuary, southern China, were collected to analyze relationships between foraminiferal distributions and environmental parameters such as salinity, depth, substrate, and water energy. A total of 123 species of foraminifera were identified. A Q-mode cluster analysis resulted in five clusters (relative abundance ≥5%), which each corresponded to a particular species association, reflecting different sub-environments: (A) the Ammonia tepida–Elphidium excavatum association, found in distributary channels and river mouths of the estuary, with low salinity, shallow water, strong currents, and comparatively coarse sediments; (B) the Ammobaculites formosensis–Cavarotalia annectens association, found in brackish waters near Lantau Island and southeastern Lingding Bay, characterizing turbid brackish-water conditions and sediment consisting of a mixture of sand-clay-silt; (C) the Haplophragmoides canariensis–Ammobaculites agglutinans var. association, found in the artificial harbor near Macao and greatly affected by human activities; (D) the Ammonia beccarii var. –Cavarotalia annectens association, mainly found in the deep channels of two bays and representing euryhaline conditions; and (E) the Ammonia tepida–Elphidium advenum association, mainly found at depths >10 m, higher salinity, low energy, and fine-grained substrate, indicating relatively stable conditions. Agglutinated foraminiferal taxa are better indicators than calcareous taxa of littoral zone environments with a mixture of sand-clay-silt substrate. Benthic foraminiferal distributions in the surface sediments were strongly influenced by salinity. Consequently, a salinity transfer function was developed using weighted-averaging partial least-squares regression. The transfer function was tested on a sediment core collected near the Modaomen distributary, with the goal to reconstruct the palaeosalinity from ~10,100 to ~5960 cal yr BP, an interval with sufficient foraminiferal tests for analysis. At ~10,100 cal yr BP, marine waters flooded the Da’ao plain. Then, a semi-enclosed estuarine environment developed and persisted until ~5960 cal yr BP. Salinity at the core site increased gradually during the early Holocene (from ~10,100 to ~8200 cal yr BP), although a short-term decrease can be recognized. The peak salinity occurred between ~8520 and 8200 cal yr BP, when brackish-marine taxa reached their highest abundances. The core site experienced declining salinity from ~8200 cal yr BP onwards as a result of strong river discharge and a decrease of marine water influence at the core site.