Rain-on-snow events can cause severe flooding in snow-dominated regions. These are expected to become more frequent in the future as climate change shifts the precipitation from snowfall to rainfall. However, little is known about how winter rainfall interacts with an evergreen canopy and affects the underlying snowpack. In this study, we document 5 years of rain-on-snow events and snowpack observations at two boreal forested sites of eastern Canada. Our observations show that rain-on-snow events over a boreal canopy lead to the formation of melt–freeze layers as rainwater refreezes at the surface of the sub-canopy snowpack. They also generate frozen percolation channels, suggesting that preferential flow is favoured in the sub-canopy snowpack during rain-on-snow events. We then used the multi-layer snow model SNOWPACK to simulate the sub-canopy snowpack at both sites. Although SNOWPACK performs reasonably well in reproducing snow height (RMSE = 17.3 cm), snow surface temperature (RMSE = 1.0 °C), and density profiles (agreement score = 0.79), its performance declines when it comes to simulating snowpack stratigraphy, as it fails to reproduce many of the observed melt–freeze layers. To correct for this, we implemented a densification function of the intercepted snow in the canopy module of SNOWPACK. This new feature allows the model to reproduce 33 % more of the observed melt–freeze layers that are induced by rain-on-snow events. This new model development also delays and reduces the snowpack runoff. In fact, it triggers the unloading of dense snow layers with small rounded grains, which in turn produces fine-over-coarse transitions that limit percolation and favour refreezing. Our results suggest that the boreal vegetation modulates the sub-canopy snowpack structure and runoff from rain-on-snow events. Overall, this study highlights the need for canopy snow property measurements to improve hydrological models in forested snow-covered regions.