Every year millions of tons of chemical products are disposed to the environment as a result of human activities, with deleterious consequences to biodiversity. In Europe the biodiversity policy basis for action is provided by the Birds and the Habitats Directives. According to these directives a network of protected areas is being built across EU countries encompassing the Natura 2000 Network. But the management plans of these protected areas do not require an ecotoxicological assessment of chemicals used within its limits. As for risk assessment protocols described in EC pieces of legislation and technical guidance documents, they are generic guidelines that not take into consideration regional particularities, e.g. the Mediterranean ecoregion specificities, and its local ecological values. Herewith we present a conceptual model for the assessment of risks posed by agriculture to bird species of conservationist concern from Natura 2000 Network sites; an example is set in a cereal steppe of the Iberian Peninsula. Hazards identified are related to the utilization of herbicides, disposal of sewage sludge to be used as fertilizer, and the input of veterinary pharmaceuticals that can be found in livestock dung and urine. This innovative model, to be used in high tier risk assessment, takes into account the biotic parameters of the protected bird species: great bustard (Otis tarda), lesser kestrel (Falco naumanni), and montagu's harrier (Circus pygargus). The transfer of chemicals is considered to occur mainly through a realistic trophic chain scenario according to the different feeding behaviour among different species and even within the same species when having different feeding habits (e.g. adults and juveniles). Moreover, the probabilistic approach is proposed in order to perform a transparent risk assessment and clearer risk communication.