Former long-term mining and smelting of pollymetallic ores in the Middle Spiš area caused a serious contamination problem of the environment with heavy metals and metalloids, especially mercury (Hg). Several studies have reported concentration of Hg in the area but this paper provides first detailed characterization of Hg contamination of different environmental components in agricultural, forest, grassland and urban ecosystems. The ecosystems are in different distances from emission sources - former mercury and copper smelting plants in NE Slovakia. Total Hg content was studied in soil/substrate samples (n = 234) and characteristic biological samples (Athyrium filix-femina (L.) Roth, Macrolepiota procera (Scop.) Singer, Boletus edulis Bull., Cyanoboletus pulverulentus (Opat.) Gelardi, Vizzini & Simonini, Triticum aestivum (L.), Poa pratensis (L.)) (n = 234) collected in the above-mentioned ecosystems. The level of contamination and environmental risks were assessed by contamination factor (Cf), index of geoaccumulation (Igeo) and potential environmental risk index (PER). To determine the level of transition of Hg from abiotic to biotic environment, bioconcentration factor (BCF) was used. To determine a health risk resulting from regular and long-term consumption of the locally available species, the results of the Hg content were compared with the Provisional Tolerable Weekly Intake (PTWI) for Hg defined by World Health Organization. The results suggest that almost 63% of the area belong to the very high risk category and 80% of the sampling sites shown very high contamination factor. Geoaccumulation index showed that almost 30% of the area is very strongly contaminated and only 8% is not contaminated with Hg. Spearman's correlation relationship confirmed that the values of PER, BCF, Cf and Igeo decreased with an increasing distance from the pollution source. The percentage of contribution to PTWI ranged between 5.76-69.0% for adults and 11.5-138% for children. Mushroom M. procera showed the highest %PTWI among the tested biological samples. Studied ecotoxicological parameters showed high level of health risk for population living in the area. Consumption of the crops grown in the area and mainly edible wild mushrooms might negatively affect the health of the consumers in the long-term.