To obtain insight into the natural variability of the coastal ecosystems off southern Kalimantan, late Holocene environmental conditions between ca. 2850 and 990 cal yr BP in the Java Sea were investigated. A 134-cm-long sediment core collected ∼50 km off the Pembuang River mouth was analysed for organic-walled dinoflagellate cysts, pollen/spores and biogeochemical parameters, e.g. organic carbon (Corg), total nitrogen (N) and calcium carbonate (CaCO3) as well as carbon and nitrogen stable isotope composition (δ13C, δ15N). Sediments consist of mixed terrestrial as well as marine organic matter, are characterised by low nutrient uptake and suggest generally low river discharge that is supported by very low pollen and spore concentrations (256 pollen grains cm−3 and 20 spores cm−3 at maximum, respectively). Foraminifera and coccolithophores dominated the plankton over cyst-producing dinoflagellates and diatoms. Dinoflagellate cyst assemblages are composed mainly of oxidation-resistant species of the genera Operculodinium and Spiniferites with a minor contribution of Impagidinium (mainly I. strialatum). The percentages of round brown and peridinioid cysts are low and decrease from the bottom of the core to the top. Palynological and biogeochemical data appear well correlated and synchronously reflect changes in the marine environment. It is reconstructed that after ca. 2480 cal yr BP, bottom waters became increasingly ventilated. A typical open-water dinoflagellate cyst association is gradually replaced by a more coastal association between ca. 2480 and 1530 cal yr BP that is most likely attributed to El Niño-induced seasonal differences between dry and wet periods of the year. After 1530 cal yr BP, a more pronounced influence of the Pembuang River is indicated by an increase in δ15N and decreased δ13C which is supported by the occurrence of nutrient-sensitive Lingulodinium machaerophorum and Nematosphaeropsis labyrinthus. The overall results indicate short-scale local environment fluctuations attributed to abiotic factors.