We investigated the utility of using synchronous measurements to create nitrogen (N) emission and retention maps of agricultural areas. Total N (TN) emissions from agricultural areas in three different Danish pilot catchments (1800–3737 ha) and within sub-catchments (100–1200 ha) were determined by a source apportionment approach. Intensive daily (main gauging stations) and fortnightly (synchronous stations) monitoring of discharge, TN, and nitrate-N (NO3-N) concentrations was conducted for two years. The groundwater N retention was calculated as the difference between a model-calculated NO3-N leaching from agricultural fields and the calculated agricultural N emission. The average annual N leaching and N emission in the three catchments amounted to 68, 48, and 58 kg N/ha and 6, 30, and 40 kg N/ha, respectively. The N retention in groundwater in the three catchments, calculated based on either TN or NO3-N emissions, amounted to 26 and 44%, 44 and 57%, and 93 and 97%, respectively, with large variations within two of the main catchments. From this study, we conclude that synchronous measurements in streams provide a good opportunity for developing local N emission and N retention maps. However, NO3-N should be used when dealing with N retention calculation at the finer resolution scale of 100–300 ha catchments
