Climate variability has major implications for marine geochemical cycles and biogenic carbonate production. Therefore, past climate-driven changes in marine environments are often inferred from geochemical data of the marine carbonate archive. Proxy calibration studies are essential for the reconstruction of such past environmental changes. Here, we use the geochemical composition of living specimens of the benthic foraminifer Ammonia tepida at three sites in a seasonally hypoxic (oxygen concentration < 63 μmol/L) marine coastal system (Lake Grevelingen, the Netherlands) to explore the use of Mn/Ca as a proxy for coastal hypoxia. The study is based on samples from three stations along a depth transect, that show contrasts in the seasonal cycle of Mn ²⁺ concentrations in the pore water of the surface sediment. In general, the sediment and pore water geochemistry of the three stations in Lake Grevelingen show increased Mn ²⁺ concentrations in late winter/spring, combined with increased Mn refluxing in summer, which are due to cable bacteria activity and bottom water hypoxia/anoxia, respectively. Laser Ablation-ICP-MS (LA-ICP-MS) allowed a comparison of Mn/Ca ratios of different parts of the benthic foraminiferal test. Our results show that higher Mn/Ca ratios are registered at the deepest station, which experiences the longest and most severe seasonal periods of hypoxia/anoxia. Additionally, the signal preserved in the central part of the benthic foraminiferal tests, which is thought to reflect the entire calcification history of the analysed specimen, appears to be driven by high pore water Mn ²⁺ concentrations due to cable bacteria activity in late winter/spring. Conversely, high Mn/Ca ratios in the last chambers reflect increased Mn refluxing in the surface sediment due to summer hypoxia/anoxia. Thus, Mn/Ca ratios of A. tepida give insight into the complex spatial and temporal variability of pore water manganese.