Boundaries are an important research theme of the ecological and social sciences and can unite diverse disciplines to advance understanding of social-ecological systems (SES). Realized and perceived boundaries exist in many forms: geographical, biophysical, political, and social. However, the nature of such boundaries and the extent to which they overlay one another to create “SES domains,” is understudied. In many cases, social and ecological boundaries may not map simply on one another, highlighting mismatches of socio-ecological domains. We propose to conduct a common suite of analyses and cross-site comparisons of the structure, function, and overlap of social and ecological boundaries in Idaho’s mid-size cities (Pocatello/Idaho Falls, Coeur d’Alene, and Treasure Valley/Boise regions). We will use multiple, pre-existing datasets and geospatial analyses to locate SES boundaries and associated domains. Within sites, we will characterize the structure of these boundaries (e.g., sharp boundary edges or gradients), address domain function regarding “hotspots” for ecosystem services, and compare and contrast boundaries across the sites. Finally, we will examine how these boundaries have historically shifted in space and time and model future scenarios (e.g., under climate change, urban development, and their interactions) to project how SES boundaries might appear and function in the future. We expect that identifying and studying SES boundaries and domains will allow us to quantify hotspots of activity and zones of social ecological conflict or cooperation that can inform future research, land management, policy, and sustainable development.