The ocean seafloor is the largest carbon reservoir within the surface Earth system, providing a valuable geochemical archive for deciphering variability in global biogeochemical cycling and climate (Ciais et al., 2013;Heinze et al., 2015). Quantification of biogeochemical cycling, especially carbon cycling at the ocean seafloor, is thus a key for understanding the fate of our future Earth (Falkowski et al., 2000;Le Quéré et al., 2018). Of vital importance in this context is the shelf seafloor, which covers less than 10% of the global ocean area (Muller-Karger et al., 2005) but has been estimated to receive ∼50% of the pelagic primary production through sedimentation (Wollast, 1991) and releases regenerated nutrients such as nitrogen, phosphorus, and silica that supply ∼80% of phytoplankton nutrient requirements (Middelburg & Soetaert, 2004). On the other hand, shelf seas constitute the most dynamic part of the surface Earth where intense interactions between geosphere, ecosphere and anthroposphere take place.

The Elbe estuary is a substantially engineered tidal water body that receives high loads of organic matter from the eutrophied Elbe river. The organic matter entering the estuary at the tidal weir is dominated by diatom populations that collapse in the deepened freshwater reach. Although the estuary’s freshwater reach is considered to manifest vertically homogenous density distribution (i.e., to be well-mixed), several indicators like trapping of particulate organic matter, near-bottom oxygen depletion and ammonium accumulation suggest that the vertical exchange of organic particles and dissolved oxygen is weakened at least temporarily. To better understand the causal links between the hydrodynamics and the oxygen and nutrient cycling in the deepened freshwater reach of the Elbe estuary, we establish a three-dimensional coupled hydrodynamical-biogeochemical model. The model demonstrates good skill in simulating the variability of the physical and biogeochemical parameters in the focal area. Coupled simulations reveal that this region is a hotspot of the degradation of diatoms and organic matter transported from the shallow productive upper estuary and the tidal weir. In summer, the water column weakly stratifies when at the bathymetric jump warmer water from the shallow upper estuary spreads over the colder water of the deepened mid reaches. Enhanced thermal stratification also occurs also in the narrow port basins and channels. Model results show intensification of the particle trapping due to the thermal gradients. The stratification also reduces the oxygenation of the near-bottom region and sedimentary layer inducing oxygen depletion and accumulation of ammonium. The study highlights that the vertical resolution is important for the understanding and simulation of estuarine ecological processes, because even weak stratification impacts the cycling of nutrients via modulation of the vertical mixing of oxygen, particularly in deepened navigation channels and port areas.

The contribution of sediments to nutrient cycling of the coastal North Sea is strongly controlled by the intensity of fluxes across the sediment water interface. Pore‐water advection is one major exchange mechanism that is well described by models, as it is determined by physical parameters. In contrast, biotransport (i.e., bioirrigation, bioturbation) as the other major transport mechanism is much more complex. Observational data reflecting biotransport, from the German Bight for example, is scarce. We sampled the major sediment provinces of the German Bight repeatedly over the years from 2013 to 2019. By employing ex situ whole core incubations, we established the seasonal and spatial variability of macrofauna‐sustained benthic fluxes of oxygen and nutrients. A multivariate, partial least squares analysis identified faunal activity, in specifically bioturbation and bioirrigation, alongside temperature, as the most important drivers of oxygen and nutrient fluxes. Their combined effect explained 63% of the observed variability in oxygen fluxes, and 36–48% of variability in nutrient fluxes. Additional 10% of the observed variability of fluxes were explained by sediment type and the availability of plankton biomass. Based on our extrapolation by sediment provinces, we conclude that pore‐water advection and macrofaunal activity contributed equally to the total benthic oxygen uptake in the German Bight.

<p><strong>Abstract.</strong> The study addresses the nitrogen cycling in Elbe estuary. Observations of salinity, nutrients and oxygen from moored stations, ship casts and helicopter surveys are presented. Observations are complemented by simulations obtained from a coupled physical-biogeochemical 3D unstructured model, applied for the first time to the estuarine environment. Model simulations reproduce the temporal variability of nutrients and oxygen along the estuarine salinity gradient. Both, observations and model results, demonstrate mostly conservative mixing of nitrate and non-conservative behavior of ammonium. Model hind-casts of the years 2012 and 2013 provide a detailed reconstruction of nitrogen recycling with ammonium appearing as the key species of the remineralisation process. Estuarine turnover processes are fueled by inputs of diatoms and organic nitrogen at the tidal weir with intense primary production manifest in the shallow river section downstream of the weir. The harbor area is the hot spot of heterotrophic decay associated with growth of meso-zooplankton, sedimentation of degradable material, remineralisation, oxygen depletion, denitrification and ammonium production. In the harbor, biochemistry shows strong vertical gradients while hydrodynamics demonstrate connectivity between the main channel and the harbor. At the estuary bed nitrogen is deposited during spring and early summer. Resuspension leads to nearly closed budget by the end of the year. During the Elbe flood in June 2013, estuarine biogeochemistry is significantly disturbed with the harbor being deactivated as hot spot of heterotrophic decay. Plankton and organic matter are flushed towards the outer estuary which in consequence sees high abundance of grazers, oxygen depletion and elevated release of ammonium.</p>

&lt;p&gt;Coastal sediments play an important role in the nutrient cycling, and the intensities of exchange processes between bottom water and pore water control the balance between sequestration and recycling of nutrients. Pore water advection as one major exchange mechanism is determined by physical parameters and thus well describable with models. By contrast, biotransport (bioirrigation, bioturbation) as the other major transport mechanism is much more complex and observational data are often scarce to quantify these processes.&lt;/p&gt;&lt;p&gt;We present ex-situ observations of oxygen and nutrient fluxes, sediment characteristics, and fauna composition over the past six years from all benthic provinces of the German Bight, which enable us to describe the spatial and seasonal variability of the benthic- pelagic coupling. We employ this dataset to detect environmental drivers of the observed variability and to test several proxies of faunal activity.&lt;/p&gt;&lt;p&gt;Our results show that abiotic parameters (sediment type, local primary production) explain the spatial variability while the dynamics of temperature and faunal activity explain the temporal variability. Effects of the complex benthic communities on benthic exchange rates can be parameterized by surprisingly simple proxies, which may help to improve benthic exchange models. By comparing in-situ measurements of pore water advection with ex situ observations, we conclude that biotransport approximately doubles the benthic- pelagic exchange rates in the German Bight.&lt;/p&gt;