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.

中文翻译：

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部分混合疏dr河口的淡水季节的季节性分层和生物地球化学转换

易北河河口是一个经过精心设计的潮汐水体，可从富营养化的易北河中吸收大量有机物。在潮汐堰处进入河口的有机物主要由硅藻组成，这些硅藻在深水淡入水中崩解。尽管认为河口的淡水河段显示出垂直均匀的密度分布（即充分混合），但一些指标（如颗粒状有机物的捕集，近底部的氧耗竭和铵盐的积累）表明有机颗粒和溶解氧的垂直交换至少暂时被削弱。为了更好地了解易北河河口深水区域中水动力与氧气和养分循环之间的因果关系，我们建立了三维耦合的水动力生物地球化学模型。该模型在模拟焦点区域的物理和生物地球化学参数的可变性方面具有很好的技能。耦合模拟结果表明，该区域是从浅层高产河口和潮汐堰坝运来的硅藻和有机物降解的热点。在夏季，当以等深线跃起时，浅层河口的较温暖的水扩散到加深的中游河段的较冷水时，水柱微弱地分层。在狭窄的港口盆地和通道中也发生了增强的热分层。模型结果显示由于热梯度导致的颗粒捕集强度增加。分层还减少了近底部区域和沉积层的氧合作用，从而引起氧气的消耗和铵的积累。这项研究强调，垂直分辨率对于理解和模拟河口生态过程非常重要，因为即使是弱分层，也会通过调节氧气的垂直混合影响养分的循环，特别是在加深的航道和港口区域。