Estuaries, being transition zones between land and ocean, act as sink or source of nitrate and thus influence the conditions in adjacent coastal waters. Hence, nitrification, which is the process oxidizing ammonium via nitrite to nitrate and simultaneously consuming oxygen, is important in estuaries. The process has been studied in sediment and water column of many estuaries, but seldom in both estuarine compartments at the same time. In August 2014, we collected water and sediment samples during a sampling trip along the salinity gradient of the hyper-turbid Ems estuary, which ends up in the North Sea. We conducted nitrification incubations in microcosms to determine nitrification potentials and we measured a suite of abiotic factors like oxygen saturation, salinity, and dissolved inorganic nitrogen (DIN). Two approaches were used, one isotope dilution method for net (NNP) and gross (GNP) nitrification potentials and one method with substrate addition for substrate induced nitrification potentials (SNP). The long-term incubation set-ups of several days include inseparably nitrification-coupled processes like remineralization and nitrate consumption, as well as cell growth, and hence they do not represent in-situ rates of nitrification. DNA was also isolated and used for quantitative PCR of the archaeal and bacterial amoA genes, which encode for the ammonia-oxidizing enzyme ammonia monooxygenase (AMO). Nitrification varied over the salinity gradient of the estuary. GNP in water and sediments decreased with increasing salinity. No NNP could be measured in the sediments of the oligohaline part of the estuary, while SNP was four-fold higher than GNP in this part of the estuary. Generally, the gene abundance of the amoA gene was higher in the oligohaline/mesohaline area than in the polyhaline area, and archaea dominated the ammonia-oxidizing communities in all samples. The local similarity in partitioning of archaeal and bacterial amoA genes over the water column and sediment at each sampling station along the estuarine gradient implied a link between the archaeal and bacterial ammonia oxidizers in both compartments, which is likely due to resuspension of sediment particles in the water column of this hyper-turbid estuary.