Deepening of estuarine tidal channels often leads to tidal amplification and increasing fine sediment import. Increasing fine sediment import, in turn, may lower the hydraulic drag (due to a smoother muddy bed and/or sedimentinduced damping of turbulence), and therefore, further strengthen tidal amplification, setting in motion a process in which the sediment concentration progressively increases until the river becomes hyper-turbid (Winterwerp and Wang, Ocean Dyn 63(11-12):1279-1292, 2013). To advance our understanding of the relative role of bed roughness and bed topography on sediment import mechanisms and sediment concentration, a Delft3D numerical model has been setup for an estuary which has been deepened and as a consequence experienced a strong increase in suspended sediment concentration: the lower Ems River. This model is calibrated against present-day hydrodynamic and sedimentary observations, and reproduces the basic sediment transport dynamics despite simplified sedimentological formulations. Historic model scenarios are semi-quantitatively calibrated against historic high and low water observations, revealing that changes in hydraulic roughness and deepening are probably equally important for the observed tidal amplification. This model is subsequently used to better understand historic changes in the hydrodynamic and sediment transport processes in the lower Ems River. Import of fine sediment has increased because of larger tidal transport, even though the degree of tidal asymmetry may not have significantly changed. The resulting rise in suspended sediment concentration reduced hydraulic drag, amplifying the tidal range. Export of fine sediment became less because the river-induced residual flow velocity decreased with deepening of the channel.

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Water temperature is an important factor determining estuarine species habitat conditions. Water temperature is mainly governed by advection (e.g., from rivers) and atmospheric exchange processes varying strongly over time (day‐night, seasonally) and the spatial domain. On a long time scale, climate change will impact water temperature in estuarine systems due to changes in river flow regimes, air temperature, and sea level rise. To determine which factors govern estuarine water temperature and its sensitivity to changes in its forcing, we developed a process‐based numerical model (Delft3D Flexible Mesh) and applied it to a well‐monitored estuarine system (the San Francisco Estuary) for validation. The process‐based approach allows for detailed process description and a physics‐based analysis of governing processes. The model was calibrated for water year 2011 and incorporated 3‐D hydrodynamics, salinity intrusion, water temperature dynamics, and atmospheric coupling. Results show significant skill in reproducing temperature observations on daily, seasonal, and yearly time scales. In North San Francisco Bay, thermal stratification is present, enhanced by salinity stratification. The temperature of the upstream, fresh water Delta area is captured well in 2‐D mode, although locally—on a small scale—vertical processes (e.g., stratification) may be important. The impact of upstream river temperature and discharge and atmospheric forcing on water temperatures differs throughout the Delta, possibly depending on dispersion and residence times. Our modeling effort provides a sound basis for future modeling studies including climate change impact on water temperature and associated ecological modeling, e.g., clam and fish habitat and phytoplankton dynamics.

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In this paper, we analyse the behaviour of fine sediments in the hyper-turbid Lower Ems River, with focus on the river's upper reaches, a stretch of about 25 km up-estuary of Terborg. Our analysis is based on long records of suspended particulate matter (SPM) from optical backscatter (OBS) measurements close to the bed at seven stations along the river, records of salinity and water level measurements at these stations, acoustic measurements on the vertical mud structure just up-estuary of Terborg and oxygen profiles in the lower 3 m of the water column close to Leerort and Terborg. Further, we use cross-sectionally averaged velocities computed with a calibrated numerical model. Distinction is made between four timescales, i.e. the semi-diurnal tidal timescale, the springneap tidal timescale, a timescale around an isolated peak in river flow (i.e. about 3 weeks) and a seasonal timescale. The data suggest that a pool of fluid/soft mud is present in these upper reaches, from up-estuary of Papenburg to a bit downestuary of Terborg. Between Terborg and Gandersum, SPM values drop rapidly but remain high at a few gram per litre. The pool of fluid/soft mud is entrained/mobilized at the onset of flood, yielding SPM values of many tens gram per litre. This suspension is transported up-estuary with the flood. Around high water slack, part of the suspension settles, being remixed during ebb, while migrating down-estuary, but likely not much further than Terborg. Around low water slack, a large fraction of the sediment settles, reforming the pool of fluid mud. The rapid entrainment from the fluid mud layer after low water slack is only possible when the peak flood velocity exceeds a critical value of around 1 m/s, i.e. when the stratified water column seems to become internally supercritical. If the peak flood velocity does not reach this critical value, f.i. during neap tide, fluid mud is not entrained up to the OBS sensors. Thus, it is not classical tidal asymmetry, but the peak flood velocity itself which governs the hyper-turbid state in the Lower Ems River. The crucial role of river flow and river floods is in reducing these peak flood velocities. During elongated periods of high river flow, in e.g. wintertime, SPM concentrations reduce, and the soft mud deposits consolidate and possibly become locally armoured as well by sand washed in from the river. We have no observations that sediments are washed out of the hyper-turbid zone. Down-estuary of Terborg, where SPM values do not reach hyper-turbid conditions, the SPM dynamics are governed by classical tidal asymmetry and estuarine circulation. Hence, nowhere in the river, sediments are flushed from the upper reaches of the river into the Ems-Dollard estuary during high river flow events. However, exchange of sediment between river and estuary should occur because of tide-induced dispersion.