In order to prepare a larger and EU-wide monitoring exercise aiming at the characterisation of processed manure as well as on the waters exposed directly or indirectly to the (processed) manure a first pilot exercise was organised to develop an appropriate protocol. While the first related report compiled a series of background information collected, the results on the analytical characterization of pilot sites operated by the Slovak University of Agriculture in Nitra are presented and discussed. Manure samples (processed and untreated), runoff, groundwater and surface water samples, were analysed for 488 compounds covering typical representatives of herbicides, fungicides, insecticides, pharmaceuticals, ingredients of personal care products and other industrially used chemicals. For 60 of these compounds (corresponding to 12 %), concentration above the established limits of quantification of these novel multi-compound technique were obtained. The study demonstrates the applicability of the hybrid target / non-target analytical approach called "Compound Fishing" and the reports presents the design for a related EU-wide exercise. Although this study does characterize the respective test sites, it delivers an understanding of environmental pressures created on sites and under real-field scenarios. The experimental work conducted allows also to establish a link between the evaluation of scientific literature, the biogeochemical modelling and the field conditions scenarios of when processed manure is applied.