Formation of lake ice is common in lakes located in mid and high latitudes. Lake ice plays a vital role in heat storage, controlling lake water temperature, survival of aquatic ecosystems, and maintaining the bio diversity of lakes. Significant warming in air temperature during the cold season (October–May) may lead to reduced ice cover of lakes and eventually disturb the lake's seasonal dynamics. We examined the role of climate variability on lake ice phenology for small inland lakes in the Great Lakes region. The Variable Infiltration Capacity (VIC) model with a physically based lake algorithm was implemented to simulate long term (i.e. 1916–2007) changes in lake ice phenology, as described by the date of ice break-up, date of ice freeze-up, and number of ice-free days. Model performance was evaluated against observed lake ice phenology. A statistically significant increase (0.08–0.21 °C) in air temperature resulted in a significant change (0.2–2.0 days/decade) in lake ice freeze-up and break-up dates. While lake ice freeze-up was strongly associated (correlation > 0.60) with air temperature of the early (October–December) cold season, lake ice break-up was highly associated (correlation = − 0.80) with air temperature during the late (March–May) cold season. The number of ice-free days was affected by the temperature changes during the entire cold season. Lakes located in the southern part of the study domain experienced stronger trends in ice phenology than those located in the northern part. Inter-decadal to decadal scale variability in the number of ice-free days not associated with long-term trends in air temperature were largely driven by the Atlantic Multi-decadal Oscillation (AMO), El-Niño Southern Oscillation (ENSO), and Pacific Decadal Oscillation (PDO).