Modelling sand/mud transport and morphodynamics in the Seine river mouth (France): an attempt using a process-based approach

The mouth of the Seine River estuary (France) has undergone marked morphological evolution over several decades mainly due to engineering works aimed at improving access to Rouen and Le Havre harbours. The intertidal areas are decreasing in size and the lower estuary is accumulating sediment and prograding. In order to understand and better describe the major morphological behaviours of the estuary, a morphodynamic numerical model was developed within the Seine-Aval program. At the end of the 1st part of the research program, a validated fine sediment transport model (3D) was available (Le Hir et al., 2001b). As the present morphological study addresses medium-term issues (a few decades), and because of the need to investigate impacts of local structures or events, we chose to use the so-called “process-based approach” starting from the existing model. First, the existing model was upgraded to account for (suspended) sand transport, and to achieve coupling between morphological changes and sediment transport. Erodability of the sediment accounts for the respective proportions of mud and sand. Simulations starting from an arbitrary surficial sediment cover show that the model is able to reproduce realistic sediment patterns. For example, it is able to change the sediment nature on the intertidal flat near Le Havre from sand to mud. Observed structures of suspended sediment are also reproduced: fine particles mainly follow the turbidity maximum whereas significant concentrations of sand grains in suspension are found where the hydrodynamic stresses are intense. Concerning morphodynamics, simulations with real forcing over one year are discussed. The effect of waves on the bathymetric evolution of the mouth is shown and the sensitivity of morphodynamics to the coupling procedure is tested.     

Breeding birds from reedbeds to alpine meadows

The main processes that determine the behaviour ofheavy metals in the Scheldt estuary are tidalhydrodynamics, sediment transport, and sorption ofheavy metals on suspended matter. The water qualitymodel WASP is applied to simulate the spatialdistribution of five heavy metals in the estuary,under average hydrodynamic and suspended sedimenttransport regimes. First, the hydrodynamical part ofthe model is constructed and the results are verifiedby comparison with measured water levels and flowvelocities. Secondly, a salt transport model is set upin order to evaluate the hydrodynamical dispersivemixing characteristics. Thirdly, a suspended sedimenttransport model is constructed and finally a transportmodel for heavy metals. The simulated distributions of the sorbedamounts of heavy metals, suspended sediment andsalinity in the estuary agree well with observations.The calculated profiles of dissolved and sorbedconcentrations of heavy metals in the water columnindicate an accumulation of heavy metals in the zoneof the turbidity maximum, while closer to the sea theconcentrations diminish due to mixing of the pollutedfluvial sediments with unpolluted marine sediments andbecause of sediment deposition in the estuary. It canbe concluded that only a small part of the heavymetals reaches the sea. This revised version was published online in July 2006 with corrections to the Cover Date.     

Modelling of water and sediment quality in the Scheldt estuary

In 1987 the Tidal Waters Division (Ministry of Transport, Public Works and Water Management, The Netherlands) initiated the SAWES project (Systems Analysis WEstern Scheldt). In the framework of this project, a water quality model for the Scheldt estuary was made. The model aims to establish the relation between pollution inputs and the concentration of pollutants in the abiotic compartments and to establish the fate of wasted substances. The model includes oxygen, nitrogen and trace metals. Due to the low oxygen content of the upper Scheldt estuary, a new model approach for trace metals had to be developed, taking into account precipitated metal sulphides. The calibration, verification and sensitivity analysis of the model provided a good understanding of the chemistry of the estuary. Afterwards the model was used to support policy making by computing how the water and sediment quality in the estuary respond to reduced inputs of waste.     

A cohesive sediment balance for the Scheldt estuary

This article present a method to generate a cohesive sediment balance for the Scheldt estuary (The Netherlands and Belgium). In this balance the net transports have been determined on a regional scale. The complicated circulation patterns on a smaller scale are considered as a black box. The cohesive sediments in the balance are defined as the inorganic sediment with a particle size smaller than 63 μm. In the balance a distinction is made between the relatively ‘clean’ marine mud fraction and the more polluted fluvial fraction. The calculations are made on a basis of field data. The field data of the morphological changes in the estuary are based on the period of 1975–1985. The net natural transport of fluvial mud is estimated to reach beyond the mouth of the estuary. The net marine import of mud is estimated to reach beyond the brackish part of the estuary, located in Belgium. The sediment balance also provides the time scale for the response of an estuary. The time scale related to the reduction in pollution proves to be quite large. Calculations with a simple analytic model with typical values for the Scheldt estuary indicate that several decades will pass until a significant improvement in bottom sediment quality is reached even after a 100% reduction of the loading of pollutants. The presented balance is not the final answer. Improvements can be achieved by more accurate field data, smaller morphological units and verification by other methods (cf. tracer methods, mathematical models).     

The mutual relationship between the monitoring and modelling of estuarine ecosystems

A general simulation model developed for the Ems estuary (a part of the Wadden Sea), to describe the main carbon flow through the foodweb, was applied for monitoring purposes. In this model, the estuary is divided into five compartments, in each of which a pelagic, an epibenthic and a benthic submodel operates. A transport model regulates the distribution of dissolved and particulate substances over the area. Two parameters that partly regulate the carbon flow are the concentrations of phosphate and of the particles (turbidity) in the water. From the sensitivity analyses for phosphate and turbidity it can be concluded that the relative effects of changes in turbidity and changes in the influx of phosphate from the rivers are large in the upper reaches and small in the lowest reaches of the estuary. This is due to the increasing influence of the coastal waters in the lower reaches. These results indicate that the reaches, which represent the beginning and the end of a gradient in the estuary, are also very suitable for monitoring the quality status of this estuary in terms of production and standing stock of groups of organisms. The need to use monitored data from the boundaries (sea and rivers) of those ecosystems as input in simulation models is discussed. Moreover, the possibilities of using simulation models to generate new ideas on the functioning of estuarine ecosystems under changing environmental conditions and to help administrators to decide on specific future management strategies are also discussed. Presented at the VI International Wadden Sea Symposium (Biologische Anstalt Helgoland, Wattenmeerstation Sylt, D-2282 List, FRG, 1–4 November 1988).     

Fish habitat use response to anthropogenic induced changes of physical processes in the Elwha estuary, Washington, USA

The Elwha River estuary has been significantly influenced by anthropogenic changes to the river, including two large dams upriver and rock dikes installed in the estuary. Together these have disrupted hydrodynamic processes and subsequent sediment delivery throughout the watershed. This article defines the functional response of fish distribution within the estuary as a result of these changes. We assessed fish distribution of three main areas of the Elwha estuary using standard beach seining techniques from March to August 2007. Species composition, ecological indices, and relative proportion of all salmonids, and in particular Chinook salmon (Oncorhynchus tshawytscha), were consistently significantly different across the estuary. Differences corresponded to a rock dike installed 30 years ago, and a sediment lens that was observed to form at the entrance to the east estuary. Sediment lenses are documented to be a common occurrence in the Elwha nearshore, and symptomatic of documented, severely disrupted sediment processes of the Elwha River. Combining the fish distribution documented in this study with the rock dike and observed sediment lens and the sediment processes documented by other researchers we, therefore, conclude: (1) Fish use within the Elwha River estuary is complex, and even fragments of connected estuary are critically important for migrating salmon; (2) Anthropogenic effects, including in river damming and diking of the estuary, can be an important ecological driver in nearshore habitat function that should be appropriately considered in estuary habitat research, management, and restoration; and (3) Juvenile salmonids appear to be able to respond to dynamic sediment environments if there are habitat options available.     

Vertical distribution of denitrification in an estuarine sediment: integrating sediment flowthrough reactor experiments and microprofiling via reactive transport modeling

Denitrifying activity in a sediment from the freshwater part of a polluted estuary in northwest Europe was quantified using two independent approaches. High-resolution N(2)O microprofiles were recorded in sediment cores to which acetylene was added to the overlying water and injected laterally into the sediment. The vertical distribution of the rate of denitrification supported by nitrate uptake from the overlying water was then derived from the time series N(2)O concentration profiles. The rates obtained for the core incubations were compared to the rates predicted by a forward reactive transport model, which included rate expression for denitrification calibrated with potential rate measurements obtained in flowthrough reactors containing undisturbed, 1-cm-thick sediment slices. The two approaches yielded comparable rate profiles, with a near-surface, 2- to 3-mm narrow zone of denitrification and maximum in situ rates on the order of 200 to 300 nmol cm(-3) h(-1). The maximum in situ rates were about twofold lower than the maximum potential rate for the 0- to 1-cm depth interval of the sediment, indicating that in situ denitrification was nitrate limited. The experimentally and model-derived rates of denitrification implied that there was nitrate uptake by the sediment at a rate that was on the order of 50 (+/- 10) nmol cm(-2) h(-1), which agreed well with direct nitrate flux measurements for core incubations. Reactive transport model calculations showed that benthic uptake of nitrate at the site is particularly sensitive to the nitrate concentration in the overlying water and the maximum potential rate of denitrification in the sediment.     

Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases.     

Macrofaunal community bioturbation along an estuarine gradient

A multidisciplinary study of the impact of bioturbation on sediment dynamics has been underway for some time at the Plymouth Marine Laboratory. The current programme has been founded upon the careful selection of six sites in the River Tamar, representative of important combinations of physical and biological variables. The paper presents preliminary results illustrating the contrasting importance of the speciesNereis diversicolor andNephtys hombergi as agents of bioturbation, given their different distributions across the six sites. Thus bioirrigation byN. diversicolor increases up the estuary and is greatest in the region of high suspended bed-load due to tidal pumping, where the consequences for chemical exchange processes between sediments and the water column may be most important. The sediment mixing effects ofN. hombergi are likely to be greater towards the seaward end of the estuary but ultimately the particular sediment types and the macrofaunal communities they support dictate the level of bioturbation in ways that do not necessarily relate to simple axial gradients along the estuary.     

Quantifying Burial,the Transport of Matter from the Lake Biosphere to the Geosphere

Burial is one of the most fundamental processes in contexts of massbalance calculations for substances (such as nutrients, organics, metals and radionuclides) in lakes. Substances can leave a lake by two processes, outflow, i.e., the transport to a downstream system, and burial, i.e., the transport by sedimentation from the lake biosphere to the geosphere. This work gives for the first time, to there best of the author's knowledge, a review on the factors and processes regulating burial and presents a general model for burial. This approach accounts for bottom dynamic conditions (i.e., where areas of fine sediment erosion, transport and accumulation prevail), sedimentation, bioturbation, mineralisation, and the depth and age of the bioactive sediment layer. This approach has been critically tested with very good results for radiocesium, radiostrontium, many metals, calcium from liming and phosphorus, but it has not been presented before in a comprehensive way. This model for burial is meant to be used in massbalance models based on ordinary differential equations (i.e., box models) in contexts where burial is not a target y‐variable but a necessary model variable (an x‐variable). This means that there are also specific demands on this approach, e.g., it must be based on readily accessible driving variables so that it is not too difficult to use the model in practice within the context of an overall lake model. The factors influencing burial, e.g., the deposition of materials and the depth of the bioactive sediment layer, are also needed in calculations of sediment concentrations and to determine amounts of substances or pollutants in sediments. To carry out such calculations, one also needs information on sediment bulk density, water content and organic content. This paper also presents new empirical models for such calculations to be used in the new model for burial.     

Aspects of modelling sediment transport and night conditions in Lake Marken

In lake Marken (Markermeer), a shallow lake in the Netherlands, sediment transport and suspended solids concentration are dominated by wind induced resuspension of sediment. The suspended solids concentration in the lake determines the attenuation of light. A 2-dimensional sediment transport model, STRESS-2d, was used to estimate the special distribution of the silt content for periods with different wind conditions. The model was calibrated using measured values of the fall velocity distributions of sediment, freshly deposited material and suspended solids. The specific light attenuation coefficient of the various sediment classes was also measured and used in the light attenuation model, CLEAR, together with simulation results from the STRESS-2d model, to simulate the light attenuation variations in time and space. By comparison of the simulation results for different scenarios, the influence of regional planning features on the sediment balance and the light attenuation can quantified. A provisional example of this method is presented.     

Effects of changes in turbidity and phosphate influx on the ecosystem of the Ems estuary as obtained by a computer simulation model

In the Ems estuary the gradients in the concentration of nutrients and in turbidity (the factors that mainly determine the amount of carbon assimilated by phytoplankton) are steep. The effects of changing the turbidity in the estuary and the amount of phosphate discharged by the rivers Ems and Westerwoldsche Aa were analysed, using the simulation model developed by BOEDE (Biological Research Ems-Dollard estuary). The results of several sensitivity runs were compared with the standard run.A 50% reduction of turbidity led to a strong increase in phytoplanktonbiomass, especially in the inner parts of the estuary where turbidity is high. On average, the effects are two to three times larger for the inner part than for the outer part of the estuary. When the turbidity doubles the opposite occurs resulting in a significant decrease of phytoplankton biomass in the upper reaches. In the lower reaches of the estuary a 50% reduction in the river discharge of phosphate is largely compensated for by changes in phosphate transport from the North Sea. This results in a nearly unchanged primary production in the lower reaches as compared with the standard run.In the upper reaches a 50% reduction of phosphate loads results in a strongly reduced primary production.In general, the zooplankton groups (copepods and microzooplankton) are influenced less than the phytoplankton. Benthic fauna is hardly influenced, except for filter feeders; which are strongly affected by the total density of the particles, a parameter which also is directly related to turbidity.     

Sediment Transport Modeling: Calibration,Verification, and Evaluation

Numerical modeling of sediment transport in fluvial and estuarine systems can be a reliable way of predicting sediment mobility. If approached naïvely, however, such modeling can produce results that do not have sufficient accuracy or reliability to be useful in decision making or design regarding a range of remediation or stabilization alternatives. It is important to recognize the numerical modeling process as merely one step toward a more complete and balanced understanding of the fluvial or estuarine system in question. Other steps include qualitative and quantitative geomorphic and engineering analyses used to evaluate the accuracy and reliability of numerical modeling as part of a three-level approach to analyze sediment mobility and overall channel behavior and trends. It must first be recognized that attempting to quantitatively analyze sediment mobility involves developing and applying simplified mathematical algorithms to the complexities of continually varying hydrodynamic and sediment transport processes through natural or modified bodies of water. Accuracy in sediment modeling can only be assessed by comparing measured data to model results with accuracy being defined as the model results matching the data within some acceptable band of uncertainty. Reliability of a sediment model is the concept of dependability in reproducing the processes one is attempting to model and implies that a model includes appropriate mathematical expressions that cover the pertinent physical processes of hydrodynamics and sediment mobility. The concept of reasonableness in sediment modeling is the evaluation of results, when compared with other independent analyses in the application of the three-level process, provide an acceptable level of consistency and consensus of conclusions. The importance of modeling software selection, data quality, model calibration, verification, validation, and reasonableness of results are discussed along with two case studies.     

Modeling of DNAPL-Dissolution,Rate-Limited Sorption and Biodegradation Reactions in Groundwater Systems

This article presents an approach for modeling the dissolution process of single component dense non-aqueous phase liquids (DNAPL), such as tetrachloroethene and trichloroethene, in a biologically reactive porous medium. In the proposed approach, the overall transport processes are conceptualized as three distinct reactions. Firstly, the dissolution (or dissolving) process of a residual DNAPL source zone is conceptualized as a mass-transfer limited reaction. Secondly, the contaminants dissolved from the DNAPL source are allowed to partition between sediment and water phases through a rate-limited sorption reaction. Finally, the contaminants in the solid and liquid phases are allowed to degrade by a set of kinetic-limited biological reactions. Although all of these three reaction processes have been researched in the past, little progress has been made towards understanding the combined effects of these processes. This work provides a rigorous mathematical model for describing the coupled effects of these three fundamental reactive transport mechanisms. The model equations are then solved using the general-purpose reactive transport code RT3D (Clement, 1997).     

Modeling of DNAPL-Dissolution, Rate-Limited Sorption and Biodegradation Reactions in Groundwater Systems

This article presents an approach for modeling the dissolution process of single component dense non-aqueous phase liquids (DNAPL), such as tetrachloroethene and trichloroethene, in a biologically reactive porous medium. In the proposed approach, the overall transport processes are conceptualized as three distinct reactions. Firstly, the dissolution (or dissolving) process of a residual DNAPL source zone is conceptualized as a mass-transfer limited reaction. Secondly, the contaminants dissolved from the DNAPL source are allowed to partition between sediment and water phases through a rate-limited sorption reaction. Finally, the contaminants in the solid and liquid phases are allowed to degrade by a set of kinetic-limited biological reactions. Although all of these three reaction processes have been researched in the past, little progress has been made towards understanding the combined effects of these processes. This work provides a rigorous mathematical model for describing the coupled effects of these three fundamental reactive transport mechanisms. The model equations are then solved using the general-purpose reactive transport code RT3D (Clement, 1997).     

Vertical Distribution of Denitrification in an Estuarine Sediment: Integrating Sediment Flowthrough Reactor Experiments and Microprofiling via Reactive Transport Modeling

Denitrifying activity in a sediment from the freshwater part of a polluted estuary in northwest Europe was quantified using two independent approaches. High-resolution N₂O microprofiles were recorded in sediment cores to which acetylene was added to the overlying water and injected laterally into the sediment. The vertical distribution of the rate of denitrification supported by nitrate uptake from the overlying water was then derived from the time series N₂O concentration profiles. The rates obtained for the core incubations were compared to the rates predicted by a forward reactive transport model, which included rate expression for denitrification calibrated with potential rate measurements obtained in flowthrough reactors containing undisturbed, 1-cm-thick sediment slices. The two approaches yielded comparable rate profiles, with a near-surface, 2- to 3-mm narrow zone of denitrification and maximum in situ rates on the order of 200 to 300 nmol cm⁻³ h⁻¹. The maximum in situ rates were about twofold lower than the maximum potential rate for the 0- to 1-cm depth interval of the sediment, indicating that in situ denitrification was nitrate limited. The experimentally and model-derived rates of denitrification implied that there was nitrate uptake by the sediment at a rate that was on the order of 50 (± 10) nmol cm⁻² h⁻¹, which agreed well with direct nitrate flux measurements for core incubations. Reactive transport model calculations showed that benthic uptake of nitrate at the site is particularly sensitive to the nitrate concentration in the overlying water and the maximum potential rate of denitrification in the sediment.     

Sea-level rise effects on macrozoobenthos distribution within an estuarine gradient using Species Distribution Modeling

The sea-level rise induced by climate change has caused impacts (e.g., floods and saline intrusion) in estuaries. In this work, we used monitoring data (salinity, sediment and taxa occurrence), simulated saline intrusion and Species Distribution Model to predict the spatial distribution of families in the estuary at two levels of SLR (0.5 m and 1 m) for two scenarios (moderate and extreme). For the simulation, we used the ensemble method applied to five models (MARS, GLM, GAM, RF and BRT). High AUC and TSS values indicated “good” to “excellent” accuracy. RF and GLM obtained the best and worst values, respectively. The model predicted local extinctions and new colonization in the upper estuarine zones. With the effects of climate change intensifying, it is extremely important that managers consider the use of predictive tools to anticipate the impacts of climate change on a local scale on species migration.     

Wave-induced sediment resuspension in the Öre estuary,northern Sweden

Material transported by the Öre River in northern Sweden is all deposited within the estuary which means that resuspension is necessary for the transport of particles out of the estuary. Wave-induced sediment resuspension in the estuary was studied by monitoring the distribution of suspended particles during a resuspension-redeposition cycle. The particle concentration in the water mass was measured with a light scattering probe, calibrated by comparison with the amount of particles collected on a filter.After a long period with calm weather and a low river input less than 100 tonne of suspended particulate matter was present in the estuary. However, during a period with stormy conditions significant resuspension of sediment particles occurred within the estuary. Two days after the storm approximately 1125 tonne of suspended particulate matter was found in the estuary. Most (61%) of the suspended matter was found in the deepest third of the water column, although up to 17% was present in the top third of the water column. The total load of particulate matter in the water column remained constant until day four after the storm, but a significant redistribution of the particulate matter occurred both in the vertical and horizontal directions. Nine days after the storm, a significant amount of particles (c. 350 tonnes) was still in suspension.     

An assessment of the potential impact of dredging activity on the Tamar Estuary over the last century: Bathymetric and hydrodynamic changes

The Tamar Estuary, S.W. England, is a commercial and military port and the site of a major naval dockyard. Parts of the estuary require regular maintenance dredging and some capital dredging has been undertaken. The estuary is also assigned Special Area of Conservation (SAC) status under the European Habitats Directive and is an important site for migrating wildfowl and wading birds. As part of an assessment undertaken for a consortium of the port operators and regulatory authorities, we have analysed the ecological, physical, chemical and socio-economic impacts of dredging on the Tamar Estuary ecosystem. This paper focuses on the physical changes through the analysis of historical survey data and the use of hydrodynamic modelling. The objective was to evaluate whether dredging has influenced the estuary morphology or hydrodynamic regime and thus impacted on the ecological habitat. Bathymetric survey data collected between 1895 and 1968 were compared with multi-beam echo sounder data obtained in 2001. The paper survey records were digitised, geo-referenced and adjusted to the modern datum and units. The accuracy and limitations of this approach are discussed. Both sets of data were contoured and analysed using a GIS package. Comparisons between 1895 and 2001 hydraulics were made using a 1-D hydrodynamic and sediment transport model set up for the bathymetry at those times but ‘driven’ using a single, common, year-long data set for tides and river flows. The results suggest that although the deep channel in the region that is mainly south of the Tamar road bridge, is on average 0.5 m deeper in 2001 than it was in 1895, this has had a negligible effect on the area of intertidal mud and, thus, on habitat available for wading birds, and minimal impact on the large-scale hydrodynamics of the estuary.