The objective of this open access book is to present protocols, methodologies, and standard operating procedures (SOPs) used for the identification of sources, transport, and fate of agro-contaminants and illustrate them with several case studies of successful applications. The Soil and Water Management & Crop Nutrition (SWMCN) Subprogramme of the Joint Food and Agriculture Organization (FAO)/International Atomic Energy Agency (IAEA) Centre of Nuclear Techniques in Food and Agriculture, through a Coordinated Research Project (CRP) in partnership with national and international research institutes, developed and evaluated a set of analytical techniques (the toolbox). The toolbox integrates multiple isotope tracers that provide information on the origins and pathways of multiple pollutants through agro-ecosystems, thereby providing more accurate guidance on mitigations. However, land management strategies to address and control the transport of pollutants from soil to water bodies remain the shared responsibility of farm and aquaculture operators, agro-chemical manufacturers, and policymakers in food and agriculture as well as the mining sectors. This book is structured into eight chapters covering (i) an overview of the book’s content, (ii) guidelines for designing water sampling programmes, (iii) the use of mixing models applicable to tracers for water pollution studies, (iv) compound-specific isotope analyses to investigate pesticide degradation in agricultural catchments, (v) the use of stable oxygen isotope composition of phosphate to investigate phosphorous in soil-plant continuum, (vi) the use of stable sulphur isotopes to disentangle agro-pollutants from other contaminants, (vii) nuclear tools used in sediment source apportionment, and (viii) the conclusions and perspectives forward. The book offers up-to-date information, and we hope it is a great source of information for students, researchers, and policymakers. The SWMCN subprogramme thanks all the contributors involved in the preparation of this publication.