Biomonitoring has been used to disclose the public health impact of contaminated sites. This study aimed at setting up good practices to apply biomonitoring targeting animal matrixes to design risk-based surveillance and exposure assessment plans. A nine-step protocol targeting farmed animals was devised and tested in three case study areas including (1) a waste dump, (2) a waste incinerator, and (3) a secondary aluminum smelter. Between 2010 and 2012, in each study area, the following 9step best practices were applied: hazard identification, GIS project creation, risk area delimitation, control area selection, receptors (livestock) identification, farms and matrixes selection, sampling study design, on-farm secondary sources exclusion, and statistical and geostatistical analysis. Dairy farms and free-range laying hens were the primary targets: eggs from both risk and control areas and milk from risk areas were sampled and submitted for detection of selected tracking contaminants compatible with the putative sources. Comparison data (risk vs. control) of heavy metal concentrations in eggs were available only for case study 2, whereas egg comparison data of persistent organic pollutants were available for all the riskcontrol pairs. After taking into account potential secondary sources, no concern from metals was arisen, whereas high concentrations of persistent organic pollutants were detected in all risk areas; however, only for the aluminum smelter case study, the contamination was broad and higher in the risk area compared with the control one. The protocol has proved to be easily applicable and flexible to varying contexts and able to provide helpful data to inform risk management decisions.