The second ADVOCATE network training workshop on the theme of Analysis and interpretation of biodegradation in soils and groundwater using physicochemical and molecular microbiological methods was hosted at AGH University of Science and Technology in Krakow, Poland, on 15/16 March 2012. The workshop was attended by 24 fellows and external participants, who included researchers, consultants and other professionals from many other countries in Europe. Over the two days the participants were introduced to the fundamental principles and practical application of advanced microbiological techniques for the assessment of contaminated environments. This included group-based exercises where each team selected two case studies to develop a conceptual model, monitoring plan and analytical framework to implement a microbiological assessment of the problem in each case. Each team then presented their interpretation and recommendations to the workshop for discussion. The workshop was presented by researchers from AGH University of Science and Technology, Warsaw University of Technology and the University of Sheffield.