Lysimeter experiments were carried out to evaluate the applicability of compound-specific isotope analysis (CSIA) for assessing transport and fate of selected herbicides in two agricultural soils cropped with corn. Monitoring of target pesticides, metabolites and tracers in drainage water made apparent the significant role of preferential flow in the mobility of the studied compounds through the soil and the vadose zone during the first days after herbicides application. The detection of metabolites in drainage water confirmed herbicides degradation once higher residence times in the soil zone where achieved. An efficient preconcentration procedure was developed for 10-L drainage water samples to achieve enough analyte enrichment for C, N and Cl isotope ratios measurements. Methods for isotope analyses are currently being developed and the applicability of CSIA for assessing the in situ biodegradation of the target pesticides during transport in soil and vadose zone will be evaluated.