Annual migrations are energetically challenging for migratory passerines and represent a potentially stressful period of the annual cycle, particularly during brief refueling periods at stopover sites. Shoreline habitats near the Great Lakes in eastern North America support many landbird migrants; however, environmental factors—including food availability and unpredictable weather—may impact the health and physiological condition of these birds during refueling periods. The aim of this study at the Braddock Bay Bird Observatory was to use key blood metrics (plasma metabolite profiling and leukocyte counts) to assess annual and within-season variation in nutrient utilization and physiological condition of 3 species of Catharus thrushes with known variation in migration strategy and passage timing. We observed similar plasma triglyceride concentrations across species; however, glucose and uric acid were elevated in a short-distance migrant, the Hermit Thrush (Catharus guttatus). Furthermore, Hermit Thrush showed higher heterophil/lymphocyte ratios than Gray-cheeked Thrush (C. minimus) or Swainson’s Thrush (C. ustulatus). Year was an important factor in all analyses exploring variables that may influence nutrient utilization or chronic stress. Our results suggest that thrushes with diverse migration strategies do not significantly differ in fat deposition patterns at the site, but end-of-season migrants may consume different resources and display increased chronic stress levels as they experience reduced food availability with the progression of autumn migration. We additionally propose that annual variation detected in this multi-year study underscores the importance of physiological condition metrics as tools for assessing yearly patterns in refueling performance at stopover sites, which is especially relevant in light of the continuing pressures of invasive species and environmental change.