A site-specific ecological risk assessment procedure for a qualitative evaluation of impairment occurring at the ecosystem level, as a result of soil contamination, was developed to integrate and visualize impairment in both terrestrial biodiversity and functional diversity and to support the decision maker in the contaminated site assessment. An Ecosystem Impairment Matrix (EcoIM) was proposed to identify the relationships between the applied measurement endpoints and the taxonomic groups living in the terrestrial system and between these taxonomic groups and the fundamental ecological processes. A specific impairment analysis procedure that used expert judgment allowed for the linking of impairment highlighted by the measurement endpoints with the terrestrial ecosystem's structure and functionality. Impairment occurring on each ecological element (i.e., biodiversity aspects and ecological functions and processes) was visualized by colored cells—1 for each relationship among measurement endpoint, taxonomic group, and ecological element—to support the expert in the ecosystem impairment evaluation. These results were then reported by the expert into the Global Ecosystem Impairment Evaluation Matrix (GEM) to summarize the obtained information and formulate a final judgment on ecosystem quality status. EcoIM and GEM were implemented in Module 2 of the decision support system DSS-ERAMANIA and are presented in this paper. The tools have been preliminarily applied to the Acna di Cengio (Italy) contaminated site; the results of this application are also presented and discussed.