It is widely recognized that biotic interactions may act as important mediators of species responses to climate change. However, collecting the abiotic and biotic covariates at the resolution and extent needed to reveal these interactions from species distribution models is often prohibitively expensive and labor-intensive. Here we used crowd-sourced environmental DNA sampling - the inference of species presence from genetic material in the environment - and high-resolution habitat covariates across 630 sites over an area of nearly 10,000 km2 to build an accurate species distribution model (AUC = 0.96; prediction accuracy = 0.90) for bull trout in cold-water habitats that incorporates fine-scale, context-dependent interactions with invasive brook trout. We then used this model to project possible climate change and brook trout invasion scenarios for bull trout forward in time. Our environmental DNA sampling results were concordant with traditional electrofishing samples in the basin and revealed species patterns that were consistent with previous studies: Bull trout were positively associated with larger stream sizes and negatively associated with high brook trout abundances. However, our modeling also revealed an important nuance: At high abundance, brook trout appear to exclude bull trout from small streams, even those below the thermal optima for brook trout. Climate projections suggest a loss of suitable bull trout habitat as streams warm and summer flows decrease, which could make deleterious interactions with brook trout more common in the future. Where brook trout are invading bull trout habitats, streams that are both large and cold are most likely to provide native bull trout with long-term refuges.