Estuaries are nutrient filters and change riverine nutrient loads before they reach coastal oceans. Their morphology have been extensively changed by anthropogenic activities like draining, deepening and dredging to meet economic and social demand, causing significant regime changes like tidal amplifications and in some cases to hyper-turbid conditions. Furthermore, increased nutrient loads, especially nitrogen, mainly by agriculture cause coastal eutrophication. Estuaries can either act as a sink or as a source of nitrate, depending on environmental and geomorphological conditions. These factors vary along an estuary, and change nitrogen turnover in the system. Here, we investigate the factors controlling nitrogen turnover in the hyper-turbid Ems estuary (Northern Germany), which has been strongly impacted by human activities. During two research cruises in August 2014 and June 2020, we measured water column properties, dissolved inorganic nitrogen, dual stable isotopes of nitrate and dissolved nitrous oxide concentration along the estuary. We found that three distinct biogeochemical zones exist along the estuary. A strong fractionation (∼26) of nitrate stable isotopes points towards nitrate removal via water column denitrification in the hyper-turbid tidal river, driven by anoxic conditions in deeper water layers. In the middle reaches of the estuary nitrification gains importance, turning this section into a net nitrate source. The outer reaches are dominated by mixing, with nitrate uptake in 2020. We find that the overarching control on biogeochemical nitrogen cycling, zonation and nitrous oxide production in the Ems estuary is exerted by suspended particulate matter concentrations and the linked oxygen deficits.