Dissolved oxygen is a key player in water quality. Stratified water bodies show distinct vertical patterns of oxygen concentration, which can originate from physical, chemical or biological processes. We observed a pronounced metalimnetic oxygen minimum in the low-nutrient Rappbode Reservoir, Germany. Contrary to the situation in the hypolimnion, measurements of lateral gradients excluded the sediment contact zone from the major sources of oxygen depletion for the metalimnetic oxygen minimum. Instead, the minimum was the result of locally enhanced oxygen consumption in the open water body. A follow-up monitoring included multiple chlorophyll a fluorescence sensors with high temporal and vertical resolution to detect and document the evolution of phytoplankton. While chlorophyll fluorescence sensors with multiple channels detected a mass development of the phycoerythrin-rich cyanobacterium Planktothrix rubescens in the metalimnion, this species was overlooked by the commonly used single-channel chlorophyll sensor. The survey indicated that the waning P. rubescens fluorescence was responsible for the oxygen minimum in the metalimnion. We hypothesize that pelagic processes, i.e., either oxygen use through decomposition of dead organic material originating from P. rubescens or P. rubescens extending its respiration beyond its photosynthetic activity, induced the metalimnetic oxygen minimum. The deeper understanding of the oxygen dynamics is mandatory for optimizing reservoir management.