Lake of the Woods (LOTW) is a large, complex lake basin once occupied by glacial Lake Agassiz. High-resolution seismic-reflection profiles and cores in the shallow, open southern basin of LOTW reveal a sedimentary architecture comprising four lacustrine units separated by three low-stand unconformities. These units represent several phases of Lake Agassiz and its changing configuration. One unconformity marks the Moorhead low phase and another marks the separation of LOTW from Lake Agassiz, perhaps ~10 cal ka BP, as the level of the latter fell, but before final drainage of Agassiz. Initially, the separate Holocene lake in the southern basin was broad and shallow, sometimes marshy or dry. Shortly after 8 cal ka BP, the southern basin dried up completely, despite the progressive rise of the northern outlet of the lake due to differential isostatic uplift. The resulting hiatus is related to the well-documented mid-Holocene arid interval in central North America. A return to wetter conditions in the late Holocene caused the southern basin of LOTW to refill since about 3800 cal yr BP. Late Holocene sediments have accumulated slightly asymmetrically in the basin, possible due to continued southward transgression of the lake as a result of isostatic tilting.