Abstract The endangered bog turtle (Glyptemys muhlenbergii) exemplifies issues related to rare species conservation; presence surveys have low detection and variables used in habitat models can lack relevance to established biological relationships of the species to its environment. The species' use of groundwater saturated soils and stream networks as core habitat and dispersal corridors has been documented. Less is known about the landscape factors that promote the formation and persistence of wetlands used for core habitat. A GIS‐based resource selection function was developed to predict bog turtle habitat use. Trained on 1 ha plots centred on occupied sites and pseudo‐absent plots constrained to areas within 56.4 m to stream network centrelines, the model tested the capacity of a topographic wetness index (TWI), stream order and soil, wetland and land cover type to predict the presence of suitable habitat and turtle occupancy. Landscape variables were sampled at 10 m resolution, but variable selection and model performance were analysed at 100 m resolution to maintain a biologically relevant 1 ha habitat scale and accommodate the resolution of other variables. Suitable habitat and turtle presence were best predicted by intermediate to high values of TWI, land cover with low vegetation height and wetlands, second‐ and third‐order streams and the occurrence of mapped National Wetland Inventory polygons and hydric soils. Very high values of TWI were negatively associated with habitat suitability. The area under the curve of the best model was 0.833. Suitable habitat was found on 88% of 55 independent sites selected using the model and nine new occupied sites were confirmed. Model error is discussed with consideration of human‐altered drainage networks on the agricultural landscape.