Groundwaters within pristine aquifers contain a low number of microorganisms, this environment being oligotrophic in most cases. Water in streams and rivers comes mainly from these aquifers. Due to human activities, more and more aquifers contains nitrate which should be considered as surprising because nitrate is a very good electron acceptor for microorganisms energy production (denitrifiers). High quantity of nitrate within aquifer should thus be regarded as a consequence of disequilibrium. It can be hypothesized for example that other elements especially a low C content should be a limiting parameter of the denitrification process. This hypothesis has been addressed within the 'InBioProcess' project using an experimental metagenomic & metaproteomic approach where the effects of changes in C/N ratio and C quality have been investigated. Furthermore, to better know the microorganisms diversity in groundwaters, a complementary analysis using mass sequencing of SSU rRNA genes has been done. Novel findings will be presented along with possible new applied aspects derivated from the environmental genomics of denitrification performed.