There is concern that subsurface drainage, by destroying or by-passing active denitrification areas, may prevent nitrate retention processes and enhance nitrate contamination of surface water by agriculture. To address this question, we studied the flow and concentration signatures of drainage waters and their transformations in a series of 5 nested watersheds, from 1 to 100 km2 area, in the Brie region near Paris(France). At all scales, nitrate concentrations are generally higher during the winter drainage season compared to the low flow periods (late spring to early fall). High nitrate concentrations characterizing drainage waters are visible at the 1st, 2nd and 3rd stream order but are diluted by surface runoff from forested zones and buffered by groundwater contributions. The analysis of nitrate chemographs and nitrate budgets established for the different nested watersheds show significant nitrogen retention. Isotopic measurements indicate that the nitrate pool is enriched in d15NNO 3 as its concentration decreases. Direct estimation of benthic denitrification with benthic chambers allowed concluding that benthic denitrification is not the only retention mechanism and that underground denitrification, affecting nitrate on its way from the base of the root zone down to the limit of the river bed, may in fact dominate nitrogen retention processes even in this intensively drained watershed.