Six years (2009–2015) of temperature and dissolved oxygen profile data show hypoxic conditions are common in the bottom waters of southern Green Bay, Lake Michigan during the summer. Depleted oxygen concentrations (<5 mg L−1) affect nearly 70% of the 38 stations sampled representing an area of ~500–600 km2. Stratification typically lasts 2+ months, from late June to early September, and some stations exhibit bottom water hypoxia (<2 mg L−1) at a frequency of nearly 25% when sampled during this period. A monitoring program initiated in 1986 by the Green Bay Metropolitan Sewerage District has provided a 23 year, recreational season record (May–September) of continuous (15 min interval) in situ bottom water oxygen and temperature measurements at the Entrance Light station of the Green Bay navigational channel. The duration of the hypoxic season ranges from 2 weeks to over 3 months at this shallow 7 m offshore site. This variability likely results from a combination of thermal stratification, oxygen consumption in deeper waters of the bay, and physical forcing mechanisms that drive cool, oxygen depleted, bottom waters on a southerly trajectory across this sensor. These data suggest the duration of hypoxic conditions may have increased during the stratified season in recent years. Hypoxia in the bay would also appear to be sensitive to relatively small changes in these forces, particularly changes in organic carbon loading and the duration of stratification.