Conventional methods that assessed the mercury (Hg) levels were not only an outcome of atmospheric pollution, but also the possibility of Hg contamination from the sample collection to laboratory analyses. Our studies used the direct mercury analyzer that measured Hg rapidly and precisely at ultra-trace concentrations with detection limit of 0.0015 ng g−1 on six favored desert plants and their surrounding soil in Kuwait. Analysis revealed elevated Hg concentrations in Tamarix chinensis Lour., and Salsola imbricate Forssk., among the chosen desert plants, especially during summer than in winter, thus labeling the qualities of a bio-indicator to Hg pollution. The overall parts-wise analysis on the six selected plants showed the elevated mean Hg concentrations in the leaves (0.89 ng g−1) followed by root (0.51 ng g−1) and stem (0.39 ng g−1) in the desert plants. Reasons attribute to the capability of these plant parts to absorb, accumulate, and assimilate Hg at varying concentrations. The overall mean Hg concentration was high in soil (2.24 ng g−1) in comparison with the mean Hg concentrations in the desert plants (0.60 ng g−1) irrespective of the two seasons. Translocation and bioaccumulation factors indicated low uptake of Hg translocation in the plant parts from the soil. Furthermore, the mean Hg concentration was found high in samples collected from Governorates (GIII) in comparison with the samples collected from other Governorates indicating the effect of pollution from various sources. The present study characterizes the selected plants as bio-indicators and also validates the impact of regional and seasonal variations to Hg pollution at ultra-trace levels in the arid ecosystem.