To better understand the primary drivers of the thermal regime in a Great Lakes estuary, and their implications for local biota, water temperature variations in the Milwaukee Estuary of Lake Michigan were studied between July and October of 2019 using a network of 25 sensors at 18 locations. Like Lake Michigan, the estuary was thermally stratified July to October, and historically dredged channels with water depths greater than 6 m allowed for the free movement of cold lake water into the estuary. However, temperatures in the estuary fluctuated rapidly both spatially and temporally, reflecting lake temperature fluctuations driven by changing meteorological conditions. Lake-driven upwelling and downwelling events influenced water temperature more than tributary contributions. Periodic upwelling and downwelling events caused temperature changes by up to 15 °C in less than 24 h. Nearshore upwelling events occasionally allowed cold, hypolimnetic lake water to reach tributary portions of the estuary beyond dredged areas, while downwelling events disrupted thermal stratification and caused the deep, dredged portions of the estuary to exceed 20 °C. Thermal impacts from these events were especially noticeable in transition zones between dredged and not dredged channels less than 2 m deep. The warming effects from downwelling persisted longer inside the estuary – up to two weeks – than cooling effects from upwelling, which typically lasted a few days. The predominantly lake-driven, rapid summer water temperature fluctuations observed in the Milwaukee Estuary serve as an important consideration in habitat restoration activities happening in Great Lakes estuaries.