The fate of contaminants in the subsurface is controlled by the complex organisation of groundwater flows. This is due to the existence of heterogeneous geological structures at different scales, such as fractures and preferential flowpaths. Accounting for these properties is particularly critical for the prediction of contaminant transport in the earth’s subsurface. The goal of the EU-funded project REACTIVEFLOWS was to develop methods for characterising and predicting contaminant transport in aquifers. REACTIVEFLOWS set about developing inverse methods for flow imaging in natural media from geophysical, flow and tracer measurements. In parallel, the aim was to develop reactive transport theories that could be tested to field cases. Novel methodologies were developed for obtaining detailed characterisation of the flow organisation in heterogeneous media. In particular, the project showed that temperature profiles can be interpreted to obtain precise flow profiles. A method based on radar imaging of saline tracer was also developed to obtain images of concentration distribution in the subsurface. REACTIVEFLOWS conducted a series of novel tracer experiments, using both non-reactive and reactive tracers. About 15 tracer tests were conducted on the fractured rock experimental site of Ploemeur, France. These test data, obtained under different flow configurations, made up a unique database from which to test dispersion and mixing models. In parallel, reactive transport experiments were performed to assess the in situ kinetics of denitrification (i.e. nitrate reduction through the use of microbes). The project has thus made progress in the development of field methodologies and realistic predictive models for transport and effective reaction kinetics. This modelling of dispersion, reaction and speciation of contaminants is key for assessing and quantifying anthropogenic impacts on groundwater systems in the framework of sustainable exploitation.