We measured dissolved and particular inorganic nitrogen concentrations in the Ems estuary (Germany). The sampling campaign was conducted on three days in August 2014 (05.08.2014– 07.08.2014) on board of the German research vessel Ludwig Prandtl. Water samples were taken regularly along the salinity gradient of the estuary irrespective of the state of the tide 2 m below the surface. For stations S276 to S280, only the Ferrybox measurements were taken 2 m below the surface. The water samples were taken by a Niskin-Bottle 2 m above the bottom. The water samples were filtered immediately and stored frozen for analysis of dissolved inorganic nutrient and nitrate stable isotope composition. Filtered samples for suspended particular matter (SPM) concentration, particular carbon and nitrogen content of SPM and nitrogen stable isotope composition of SPM were dried at 50°C and also stored frozen. An onboard membrane pump provided the on-line in situ FerryBox system with water from 2 m below the surface. It continuously measured oxygen, salinity, and temperature during our cruise. More information can be found in Sanders and Laanbroek (2018). The aims of the cruise were 1) to study spatial segregation of nitrogen turnover, 2) to identify the dominant nitrogen turnover processes in the water column and 3) to investigate controlling factors of the nitrogen cycle along the Ems estuary.