Chamber and micrometeorological mercury flux data collected during the Nevada STORMS intercomparison study were used to identify natural and methodological factors controlling data variability. Micrometeorological and chamber measurements revealed that flux variability at a site is closely related to the Hg concentrations in the substrate, which were found to vary with mineral composition, grain size, and sampling depth. Environmental factors also influenced flux variability. Following two rainfall events, fluxes measured by chamber and micrometeorological methods increased substantially. The micrometeorological flux was enhanced five fold following the rain event. Fluxes measured by both methods were also influenced by net radiation and temperature as evidenced by their tendency to follow the diel cycle in these variables. Day-time fluxes were 6 times greater than nighttime fluxes. Data analysis revealed that interactions between environmental and geochemical variables complicate relationships between the flux and these variables. Understanding the variability at a flux monitoring site is important to establish relationships for scaling up and for the development of consistent sampling protocols that allow comparisons from one study to another and adequately quantify mercury fluxes from natural sites to provide representative emission data that can be used for scaling up to regional and global scales.