Firefighters are frequently exposed to high temperatures, environmental toxicants, and strenuous physical demands. The health impacts of these occupational exposures on processes including inflammation and kidney function as well as on the gut microbiota are poorly understood. A firefighter training course may provide a controlled environment to assess these health risks. Basic health measures, stool, and blood samples were obtained from 24 firefighters participating in a one-week, heat-intensive training course. Indicators of inflammation, gut permeability, kidney health, and stool microbiota composition were measured before and after the training course in 18 participants. Urine specific gravity was measured before and after a heat-intensive training day to evaluate dehydration. The majority of firefighters in this cohort were categorized as hypertensive and experienced multiple heat-related illness symptoms during the training week and dehydration after the heat-intensive training day. While plasma IL-1β, CXCL8, and NGAL decreased over the training week, other indicators of inflammation and acute kidney injury increased, and estimated kidney function declined. Microbiota composition shifted over the course of the training week, with changes in Peptostreptococcus anaerobius and Streptococcus. This pilot study conducted in a controlled field setting suggests that the occupational environment of firefighters may increase their risk for systemic inflammation and kidney disease.