This training workshop on the theme of Application of innovative methods for site characterisation, water and contaminant flux measurement in the subsurface was hosted at the UFZ Leipzig, Germany, on 19/20 June 2012. The workshop was attended by 31 fellows and external participants, who included researchers, consultants and other professionals from Europe. Over the two days the participants were introduced to many different approaches and technical concepts to characterise and sample properties of the subsurface environment which influence contaminant transport and remediation performance. This included sessions on the application of novel tracer techniques, remediation strategies using nanoparticles and radiofrequency heating, and mass flux approaches for groundwater sampling and remediation performance assessment. The use of constructed wetlands for sustainable remediation, treatment technologies for industrial wastewater and the complex issues of managing contaminated landscapes was also covered. A field excursion provided the opportunity for participants to view innovative sustainable wastewater treatment technologies and visit demonstration sites hosting long-term pilot-scale studies of in situ bioremediation concepts for industrial organic chemicals and ammonium-contaminated wastewater. The workshop was presented by researchers from the Helmholtz Centre for Environmental Research UFZ, University of Liege and VITO, and staff from Stadtentwaesserung Dresden and LAF Magdeburg, both associated partners in the ADVOCATE network.