Monitoring of agricultural mini-catchments has been part of the Danish national monitoring programme (NOVANA) since 1989. Thus, nitrogen (N) concentrations and loads have been monitored in soil water, tile drains, and streams within five agricultural mini-catchments. Moreover, extensive monitoring of N concentrations and loads in streams draining 46 mini-catchments has been conducted every year since 1989. This has resulted in two national datasets on trends in flow-weighted N concentrations relative to factors such as groundwater age and management history. We analyzed these datasets and found that the intensively monitored micro-catchments generally showed a strong signal with significant downward trends in flow-weighted N concentrations in monitored soil water (−22% to −68%), tile drains (−38% to −59%), and streams (−19% to −53%). The 46 micro-catchments monitored for N in streams also exhibited downward trends in flow-weighted N concentrations, which can mainly be ascribed to the introduction of mandatory national regulation of N in agriculture in Denmark in the mid-1980s. However, classification of the mini-catchments according to the age of the oxidized groundwater revealed significant differences in N trends between the groups of mini-catchments. Thus, the strongest downward trend in flow-weighted N concentrations was as follows: <1 year (−52%), 1–3 years (−44%) and >3 year (−38%).