Fish populations at the fringe of their geographic range often inhabit marginal habitats and are vulnerable to ecological disturbances such as species invasion, land cover conversion, and climate change. The Driftless Area of northeastern Iowa, USA, represents the southwestern edge of Brook Trout’s Salvelinus fontinalis native range, where endemic populations have been greatly reduced due to habitat degradation and introduced Brown Trout Salmo trutta. Therefore, documenting Brook Trout occurrence patterns at the southern tip of their range may prove useful for the conservation of peripheral populations. We fit single species occupancy models at multiple spatial scales to estimate the relative effects of biotic (e.g., Brown Trout density) and habitat (instream, riparian, and watershed) variables on Brook Trout and Brown Trout occupancy to predict their current distribution in the Iowa Driftless Area. Species occurrence and physical habitat data were collected at 138 stream segments of the Upper Iowa, Yellow, and Little Maquoketa watersheds (HUC8) during May through September, 2018 and 2019. Brook Trout occupancy was low (19 of 138 sites) and affected by local (instream and riparian) habitat covariates, particularly August-September stream temperatures, but no adverse effects of Brown Trout density were detected. Brown Trout occupied 54% of streams (74 of 138 sites) and occupancy was influenced by a combination of local (mean stream velocity, the percentage of run macrohabitat, and August-September stream temperatures) and catchment-scale (percent forested land cover and upstream catchment area) habitat variables. Our results provide evidence that instream thermal conditions are a critical determinate of Brook Trout distribution while Brown Trout exhibit plasticity in habitat suitability and increased colonization in areas where introduced. Given Brook Trout’s dependence on cold stream temperatures, the projected loss of thermally suitable habitats due to climate change may facilitate their replacement by naturalized Brown Trout at the southwestern extent of their range.