Benthic fluxes and water column distributions of dissolved inorganic nitrogen (DIN) and total dissolved phosphate (PO43−) were measured in situ at 7 sites across a redox gradient from oxic to anoxic bottom waters in the Eastern Gotland Basin (Baltic Sea). The study area was divided into the oxic zone (60 to ca. 80m water depth, O2>30μM), the hypoxic transition zone (HTZ, ca. 80 to 120m, O2<30μM) and the deep anoxic and sulfidic basin (>ca. 120m). Sediments in the HTZ were covered by mats of vacuolated sulfur bacteria. Ammonium (NH4+) fluxes in the deep basin and the HTZ were elevated at 0.6mmolm−2d−1 and 1mmolm−2d−1, respectively. Nitrate (NO3−) fluxes were directed into the sediment at all stations in the HTZ and were zero in the deep basin. PO43− release was highest in the HTZ at 0.23mmolm−2d−1, with a further release of 0.2mmolm−2d−1 in the deep basin. Up-scaling the benthic fluxes to the Baltic Proper equals 109ktyr−1 of PO43− and 266ktyr−1 of DIN. This is eight- and two-fold higher than the total external load of P (14ktyr−1) and DIN (140ktyr−1) in 2006 (HELCOM 2009b). The HTZ makes an important contribution to the internal nutrient loading in the Baltic Proper, releasing 70% of P (76ktyr−1) and 75% of DIN (200ktyr−1) despite covering only 51% of area.