The expansion of transient and permanent coastal benthic anoxia is one of the most severe problems for the coastal ocean globally. We report frequent, hidden hypoxia in the bottom 5 cm of the water column of a coastal site in the central Baltic Sea by continuous high-resolution profiling of oxygen (O2) directly above the sediment surface. This hypoxia stood in stark contrast to 30-yr O2 monitoring records at this site that suggest apparent continuous well-oxygenated conditions. In situ measurements showed highly dynamic conditions in the bottom 30 cm recording frequent gradual and abrupt changes between normoxic (> 63 μmol L−1) and hypoxic (< 63 μmol L−1) conditions that would remain undetectable by conventional bottom water O2 monitoring. The temporal variability of these “hidden” hypoxia is tied to the dynamic current field and to changes in O2 consumption following resuspension events. Our observations suggest that transient benthic hypoxia is much more common than routine monitoring data indicate.