Pollutants affecting visibility at Craters of the Moon include a mix of agricultural, industrial, and vehicle emissions. Agricultural-related emission sources include stubble field burning and plowing, primarily from agricultural activities in the Snake River Plain. Largest urban areas with associated vehicle and other urban emissions are Boise, Twin Falls, and Idaho Falls/Pocatello. Other emission sources include the Idaho National Laboratory, a DOE nuclear research center 25 km (15 mi) east of the area that has several permitted point sources of NOX and SO2, and large mineral and chemical plants in the Pocatello area 100 km (60 miles) to the southeast. High aerosol concentrations may result from regional wildland fires.

Data comparing the best and worst visibility days at Craters of the Moon show poor visibility most often occurs in the winter; when air stagnation events create inversions, conditions cause pollutant levels to rise. During these episodes, visibility is impacted by higher levels of nitrates and sulfates, which contribute to the formation of fine particulates. In the summer, visibility impairment occurs less frequently. Visibility impairment in the summertime is due to higher levels of organic matter, attributed to wildland fires.