Pollutants inhibit thallus growth and development or alter the metabolism and associated anatomical and morphophysiological characteristics of lichens. Since agricultural matrices can act as sources of pollution by dispersing agrochemicals to vegetation fragments, this study tested the hypothesis that Parmotrema tinctorum can serve as the indicator of edge effect in such fragments. In other words, we assumed the impact of pollutant accumulation to be greater at the vegetation edges and explored the utility of this lichen as a bioindicator of pollutants dispersed from agricultural matrices. Differences in the anatomical layers of P. tinctorum thalli sampled from the edge and center of four vegetation fragments (CER, SSF, SSC, and ENP) were evaluated, and the effects of agricultural matrices on macro- and micronutrient levels, heavy metal levels, and photosynthetic pigment content were analyzed. Anatomical layers were thicker in P. tinctorum thalli from the edges of SSC and ENP, indicating the need for photobiont protection at these sites. Edge effect was observed on Al accumulation in the thallus, indicating dispersion of this metal from agricultural matrices and its greater impact in the edge populations. Edge effect was also evident on photosynthetic pigment content, macro- and micronutrient levels, and heavy metal concentration in the thallus, and the values reflected high ecological imbalance currently verified at the edge of ENP, an area of permanent protection. In areas within ENP, chlorophyll a/b ratio reflected stress factors acting on the thallus, indicating that even legally protected areas are not free from the impact of atmospheric pollutants. P. tinctorum may serve as an effective indicator of edge effects and may be used for biomonitoring pollutant dispersion from agricultural matrices.