Many aquatic ecosystems are experiencing a decline in their oxygen (O 2 ) content and this is predicted to continue. Implications of this change on several properties of bacterioplankton (heterotrophic prokaryotes) remain however are poorly known. In this study, oxic samples (∼170 μM O 2 = controls) from an oligohaline region of the Scheldt Estuary were purged with N 2 to yield low-O 2 samples (∼69 μM O 2 = treatments); all were amended with 13 C-glucose and incubated in dark to examine carbon incorporation and cell size of heterotrophic prokaryotes, and relationships between organic matter (OM) degradation and phosphate (P) availability in waters following O 2 loss. Stable isotope ( 13 C) probing of phospholipid fatty acids (PLFA) and flow cytometry were used. In samples that have experienced O 2 loss, PLFA biomass became higher, prokaryotic cells had significantly larger size and higher nucleic acid content, but P concentrations was lower, compared to controls. P concentration and OM degradation were positively related in controls, but uncoupled in low-O 2 samples. Moreover, the dominant PLFA 16:1ω7c (likely mainly from Gramnegative bacteria) and the nucleic acid content of heterotrophic prokaryotic cells in low-O 2 samples explained (62-72 %) differences between controls and low-O 2 samples in P amounts. Shortly after incubations began, low-O 2 samples had consistently lower bacterial PLFA 13 C-enrichments, suggesting involvement of facultatively anaerobic metabolism in carbon incorporation, and supporting the view that this metabolic pathway is widespread among pelagic bacteria in coastal nutrientrich ecosystems. Estimates based on 13 C-enrichment of PLFAs indicated that grazing by protozoa on some bacteria was stronger in low-O 2 samples than in controls, suggesting that the grazing pressure on some heterotrophic prokaryotes may increase at the onset of O 2 deficiency in nutrient-rich aquatic systems. These findings also suggest that physiological responses of heterotrophic prokaryotes to O 2 loss in such ecosystems include increases in cell activity, high carbon incorporation, and possibly phosphorus retention by cells that may contribute to reduce phosphate availability in waters.