A 9200-year-long Holocene record of pollen, magnetic susceptibility (MS), and sedimentation rates from Pup Lake, northern Lower Michigan, USA, along with comparative pollen data from regional paleoecological sites and optically stimulated luminescence dates from inland sand dunes across the Great Lakes region, reveals emerging relationships among climate, vegetation, and erosion. Tsuga (hemlock) pollen was used to track local- and regional-scale hydroclimate variability owing to the taxon’s moisture sensitivity and close association with modern lake-effect snowfall gradients. Two periods of elevated MS and Tsuga values, 6800–5200 cal yr BP and 3200–800 cal yr BP, are interpreted as millennial-scale phases of greater effective moisture that drove key changes in forest composition and resulted in accelerated erosion. Overall, the lake’s MS record broadly tracks changes in Tsuga pollen frequencies and sedimentation rates, particularly during the Late Holocene, suggesting the emergence of a well-defined lake-effect climate system between 5200 and 1000 cal yr BP. Additionally, Pup Lake’s MS record exhibits notable connections with widely recognized hemispheric-scale climate deterioration episodes, including the 9.2, 8.2, and 5.2 ka BP events.