A summary is provided of the first of a series of proposed Integrated Science Initiative workshops supported by the UNESCO International Hydrological Programme. The workshop brought together hydrologists, environmental chemists, microbiologists, stable isotope specialists and natural resource managers with the purpose of communicating new ideas on ways to assess microbial degradation processes and reactive transport at catchment scales. The focus was on diffuse contamination at catchment scales and the application of compound-specific isotope analysis (CSIA) in the assessment of biological degradation processes of agrochemicals. Major outcomes were identifying the linkage between water residence time distribution and rates of contaminant degradation, identifying the need for better information on compound specific microbial degradation isotope fractionation factors and the potential of CSIA in identifying key degradative processes. In the natural resource management context, a framework was developed where CSIA techniques were identified as practically unique in their capacity to serve as distributed integrating indicators of process across a range of scales (micro to diffuse) of relevance to the problem of diffuse pollution assessment. Copyright ?? 2006 John Wiley & Sons, Ltd.