Air quality at Agate is unimpaired and the visibility is good for the area. John Ray (2002; cf. EPA 2000), NPS Air Quality Specialist, estimates that over the past five years the ozone levels at Agate have been below the Environmental Protection Agency's Primary Standard, with the fourth highest annual daily eight-hour maximum ozone level being 68-75ppb (85% of the current National Ambient Air Quality Standards) and the average annual daily one-hour maximum at 87-98ppb (74% of the older Standard).

An ozone monitoring station was installed at Agate Fossil Beds in 2007.   The information collected from this station may be accessed here.