Despite considerable investment in recent years, approximately half of all Irish water bodies still do not meet Water Framework Directive (WFD; European Parliament and Council, 2000) objectives.Identifying appropriate measures to address eutrophication linked to agriculture remains a major challenge. Field and modelling studies were integrated in two hydro(geo)logically contrasting Irish catchments at less than Good status, to identify the main pathways delivering flow and nutrients to streams. The transport of phosphorus (P) via overland flow and interflow, and from small point sources, proved the key issues in the catchment underlain by poorly draining soils. Measures in such catchments need to focus on intercepting pathways and mitigating the discharges. In the freely draining karstified catchment, transport of nitrogen (N) and P via subsurface pathways were the key issues. Measures for N in these scenarios need to focus on best management practices of source loads, as interrupting the pathway is much more challenging, whereas measures for P must target managing inputs to groundwater, for example via sinking streams from poorly draining areas. Achieving successful WFD outcomes depends on having a site-specific, three-dimensional understanding of contaminant transfer pathways.