Aeolian studies of Lake Michigan’s coastal dunes have yet to elucidate what factors control their episodic activity over the past 5000 years. High lake levels exposing sand along with increased storminess is generally accepted for high perched dunes. This hypothesis, however, remains poorly tested for low perched dunes along the southeast Lake Michigan coastline. Here, small lakes in the lee of dune complexes contain aeolian sand and various biological proxies. Age and sedimentation rate models from Gilligan Lake cores guide analysis of aeolian sand, charcoal, pollen, and diatoms at high resolution (1 cm [10.4 yr/cm]) during the high-water Algoma Phase (3.1–2.4 ka) of the upper Great Lakes. The diatoms record a transition from a deep, more acidic lake to a shallower, more alkaline lake with fewer wetlands. This transition is accompanied by a stepped increase in the amount of aeolian sand. There is a weak correlation (R2 0.5, p < 0.01) between increasing abundances of charcoal chunks and sand. Peaks of sand follow peaks in charcoal threads and sheets, suggesting fire played a role in removing vegetation, presaging the landscape for increases in storminess. Arboreal pollen records a transition from a mesic forest Fagus-Acer-Quercus-Abies assemblage suggestive of moister conditions to one richer in mesic hardwoods tolerant of drier conditions. Together, the environmental proxy data record a shallowing lake concomitant with increasing aeolian sand, suggesting that drought-like conditions along the coastline conditioned the landscape for renewed aeolian activity. Once initiated, increased storminess and shoreline erosion maintained dune activity through increased sediment supply.