The built environment contributes to an individual’s health, and rural geographies face unique challenges for healthy eating and active living. The purpose of this descriptive study was to assess the nutrition and physical activity environments in rural communities with high obesity prevalence. One community within each of six high obesity prevalence counties in a rural Midwest state completed the Nutrition Environment Measures Survey for Stores (NEMS-S) and the Rural Active Living Assessment (RALA). Data were collected by trained community members and study staff. All communities had at least one grocery store and five had at least one convenience store. Grocery stores had higher mean total NEMS-S scores than convenience stores (26.6 vs. 6.0, p < 0.001), and higher scores for availability (18.7 vs. 5.3, p < 0.001) and quality (5.4 vs. 0, p < 0.001) of healthful foods (higher scores are preferable). The mean RALA town-wide assessment score across communities was 56.5 + 15.6 out of a possible 100 points. The mean RALA program and policy assessment score was 40.8 + 20.4 out of a possible 100 points. While grocery stores and schools are important for enhancing food and physical environments in rural areas, many opportunities exist for improvements to impact behaviors and address obesity.