Accurate modelling of subsurface soil temperatures in the boreal shield is essential for characterizing species at risk nesting habitat. Various turtle species (e.g. Emydoidea blandingii, Chelydra sepentina, Clemmys guttata) in the boreal shield use these thin soil deposits to lay their eggs. Suitable nest temperatures for successful hatching are directly related to the hydrophysical properties of the soil and the morphology of the surrounding bedrock. The relative proportion of water in the soil surrounding the nest controls the thermal buffering to extreme temperature swings which can lower hatch success, while adequate drainage following rain events is critical to prevent eggs from drowning. This work uses the biophysical model NicheMapR, to model soil temperatures in these thin soil deposits to assess future climate change impacts on nest site temperatures. The objectives of this work are to (1) assess NicheMapR’s capabilities and parameter sensitivity when modelling nest temperatures of known turtle nest sites, and (2) quantify how a warming climate may shift nest site conditions. This interdisciplinary approach combines hydrological sciences with turtle ecology, and provides key insights for rights holders and stakeholders when working towards conservation goals for species at risk in the boreal shield.