Compound-specific isotope analysis (CSIA) is a valuable tool to track and quantify pollutant degradation in environmental systems. However, some analytical challenges still restrict the possibility to exploit its full potential. Moreover, to give a sound base on CSIA application in real-case studies, it is crucial to understand the transformation processes of pesticides and their associate isotope fractionations. The EU-funded ISOTOPEST project aims to optimise extraction and analytical methods for measuring isotope ratios in the triazine herbicide atrazine and the organochlorine insecticide methoxychlor, an unexplored pesticide of high environmental concern. The project aspires to increase the database of isotope fractionations to bring further demonstration of CSIA in field studies, and to provide a monitoring, water management and remediation tool.