Oxygen conditions is a fundamental variable for aquatic life. However, a succession of mild winters has hindered the complete mixing of the waters in Lake Geneva, thus limiting the mixing of surface waters with deep waters and reducing the annual oxygen recharge in the hypolimnion. Further, low oxygen supply has not compensated for the biological and chemical oxygen demand, leading to the onset of hypoxic conditions during autumn and the spread of oxygen condition below 4 mg O2 L‐1 as recommended by the Swiss regulations. Despite the occurrence of hypoxia observed over the last years at the deepest point of the lake (SHL2 station, information to characterise the spatial extent of hypoxic waters is still very limited. In this study, eight vertical physico‐chemical profiles were carried out in the water column following two transects in the fall of 2022 in order to map the extent of hypoxia in the hypolimnion. APHOX‐LX probe data indicate that the threshold of 4 mg O2 L‐1 was reached between depths 211.6 and 245.3 m according to the profiles studied (corresponding to the minimum and maximum depths of the stations studied, respectively 215.8 m and 309.6 m). Therefore the distribution of oxygen concentrations is not horizontal, but rather tends to present a curved distribution. Low oxygen conditions in Lake Geneva have larger spatial extent than previously suggested by monthly monitoring in SHL2. This study suggests a current limitation in the oxygen monitoring protocol which is not suitable for studying the conditions in the waters near the sediment interface. This limitation compromises our understanding of the oxygen conditions in the hypolimnion, but also potential effects on benthic habitats or internal phosphorus and trace metal loads.