Water movements due to temperature gradients and short-term water level fluctuations control the flushing timescale of the many shallow embayments in the Great Lakes. In this article the water circulation within Frenchman's Bay is reported and estimates made of the hydraulic flushing timescale. This shallow freshwater embayment is permanently connected to Lake Ontario through a channel of width 30 m and depth of 2 m. The water flushing timescale is estimated by using a salt mass budget, leading to a flushing timescale of 7–10 days. During the summer, the exchange of water between the bay and the lake can be driven by a combination of horizontal thermal gradients, and by small but ubiquitous 1–5 cm oscillations in the water level of Lake Ontario. The water movements that are predicted due to water level fluctuations (caused by seiches, storm surges and tides) and due to horizontal thermal gradients leads to estimates of the flushing time of water within Frenchman's Bay in the range of 12–13.5 days, i.e. the same order of magnitude as the salt budget. One consequence of the temperature driven exchange flows is to cause strong and persistent temperature stratification within the bay, which in combination with high nutrient loading and low winds in summer leads to frequent anoxic events.