This publication is intended to support the proper use of the compound specific stable isotope (CSSI) technique for identifying sources of sediment within agroecosystems. Based on the measurement of carbon-13 natural abundance signatures of fatty acids in the soil, this technique allows users to determine and apportion the sources that originate from different land uses. While covering the fundamental concepts of the CSSI technique, this publication is unique in providing step-by-step instructions for scientists, technicians and students on how to effectively use this isotope approach. This comprehensive illustrated guide highlights new opportunities for improving area-wide soil conservation strategies in fragile agricultural landscapes.