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Sediment is an integral and dynamic part of aquatic systems and it plays a major role in the hydrological, geomorphological and ecological functioning of river basins, defined here to include lakes, reservoirs, estuaries and the coastal zone. In natural and agricultural systems, sediment originates from the weathering of rocks, the mobilization and erosion of soils and river banks, and mass movements such as landslides and debris flows. In most river basins there are also important contributions to the sediment load of organic-rich material from a range of sources such as riparian trees, macrophytes and fish. This inorganic and organic material is susceptible to transportation downstream by flowing water, from headwaters and other source areas towards the outlet of the river basin. Flow rates decline in lowland areas (and areas where flow is reduced) where transported material settles in slack-zones and on the bed of the river, and on river floodplains during overbank events. At the end of the river much of the sediment is deposited in the estuary and on the seabed of the coastal zone.

Sediments play an important role in river engineering and water resources management. In the past, many rivers in developed countries have been engineered by training and regulation works for navigation, hydropower generation and flood protection. In the past decades, municipal and industrial waslewaler discharge and various diffusive sources from agriculture have caused a widespread contamination of river sediments by heavy metals, organic toxicants and agrochemicals. Meanwhile, many historically contaminated sites in rivers are localized and identified as a severe latent hazard for the river ecosystem (see Sect. 1.1.3). Most of the contaminated sites have been detected in low flowing water bodies which are either permanently or temporarily connected to the main river channel such as near bank groyne fields in waterways or harbors, river dead arms, flood plains and last not least flood retention reservoirs (Fig. 2.1). Many deposits are most likely to be resuspended and transported over a long distance by extreme discharges causing contamination of not yet polluted surface water bodies and unpolluted soils subject to flooding.

Few studies in the literature compare the sediment stability of depositional habits across marine, freshwater and brackish ecosystems. This is partly because there is conceptual difficulty in comparing different erosional devices but also because scientist often focus on specific habitats. In addition, many field devices generate shear stresses over the 0–1 N m range, with few capable of generating erosive forces beyond this level (). However, habitats such as intertidal deposits and salt marshes are often quite resistant to hydrodynamic forcing and are considered to provide an “ecosystem service” of coastal protection. Most existing measurements have been made within a “measurement comfort zone” (Fig. 3.1), usually where a bed shear stress between approximately 0.1 and 1 N m surpasses the critical threshold. However, the study of a wider range of habitats is fundamental to the understanding of ecosystem dynamics in aquatic environments.

Contaminants such as heavy metals or organic pollutants are adsorbed to fine sediment particles which are transported through the river system and deposited in the regions of low flow velocities. This results in potential sources of contaminants called “hot spots” which can be eroded by floods causing deterioration of the river water quality. Therefore, the erosion, transport and deposition of contaminated sediments play a significant role in water resources engineering and management. It is a challenging task to model and predict the pathway and fate of contaminated sediments with emphasis on their spatial and temporal distribution in surface waters.

The Water Framework Directive (WFD) sets ambitious objectives for the protection of European water resources (). For priority substances and other pollutants environmental quality standards have been defined for surface water. An understanding of the sources and pathways of these substances within river catchments is crucial to establish effective monitoring programs and to develop emission control strategies as a part of cost-effective programs of measures. In this context, source-related emission modeling offers the potential to support WFD implementation, since these catchment models provide annual load balances and highlight the relevance of various pollutant sources and pathways (Fig. 5.1).

The settling and storage of fine-grained sediments in the interstices of fluvial gravel beds can have significant implications on both sediment conveyance in catchments and aquatic habitat quality. Given that suspended fine-grained sediment (<263 μm) moves not only as individual particles, but also as particle aggregates or flocs, there has been a relatively recent research emphasis on characterizing these structures and the conditions which enhance their growth and settling in freshwater aquatic environments (; ; ; ; ; ).

The understanding of the transport of cohesive sediments in flowing waters is one of the major tasks in fluvial hydrology. The bulk of material is transported during events as suspended particulate matter, but a continuous exchange with the river bottom and its interaction with the transport mechanisms of coarse material make it difficult to distinguish between different processes. From the water chemistry point of view highest concentrations of dissolved solids normally occur under dry weather flow conditions, when the concentrations of suspended particulate matter are lowest and the river bottom is supposed to behave as a sink. What is insignificant for the transport of most of the material can be crucial for understanding the fluxes between water body, suspended particles and river bottom.

Many of the sediments in our coastal environments are contaminated with various metals. The highes Iconcenlralionsofconlaminanls are found in harb ours, where anlifouling painls and industrial activities are the main sources. In the past years there has been a strong focus on TBT that is known to be highly toxic and to affect the hormonal balance of many animals. Almost all substitutes for TBT are based on Cu-complexes. Copper is known to form strong complexes with natural organic matter and the total Cu-concentration in sediments is found to correlate with the concentration of organic matter (see Fig. 8.1).

Natural sediments are not sterile but inhabited by a large range of microorganisms () and higher forms of life. As a consequence, these organisms participate in many chemical processes in sediments, in the interaction between sediments and the water phase and in sediment dynamics. In fluvial environments, the interface between the major water body and the sediment, is a very active zone both in physicochemical and biological terms. Especially in highly permeable sediments, the dynamic flux of energy, nutrients, metabolites and particles (including microorganisms) is interdependent with local hydrodynamics (). Due to their slime matrix, active microbial communities at the water-sediment interface, develop into macroscopic scale structures which modify sediment topography and frictional resistance. These surface alterations have repercussions in fluid flow, shear forces and other physical parameters, especially at the benthic boundary layer. Microbial colonization is not limited to the sediment-liquid interface; equally important on their effect on river sediment hydrodynamics, is their ability to develop at significant sediment depths. At this level, permeability and hydraulic conductivity changes caused by microbial colonization, can have a profound effect on sediment cohesion and sorption/ desorption processes (Leon-Morales et al. this vol.).

The overall goal of a well-designed and well-implemented sampling and analysis program is to measure accurately what is really the status of the area studied. Environmental decisions are made on the assumption that analytical results are, within known limits of accuracy and precision, representative of site conditions. Many sources of error exist that could affect the analytical results. These sources of error may include sample collection methods, sample handling, preservation, and transport; personnel training; analytical methods; data reporting; and record keeping. Therefore, a quality assurance program has to be designed for each sediment quality evaluation to minimize these sources of error and to control all phases of the monitoring process.