Over the years, Lake Markermeer, formerly a sea arm of the North Sea, has experienced a decline in some of its ecological values. A high suspended sediment concentration in the water column of the lake is believed to be one of the causes of this ecological deterioration. Currently, short term suspended sediment dynamics are well understood. This is reflected in the model of van Kessel (2008), which properly describes variations in short term suspended sediment concentrations. However, it is hypothesized that the long term behavior may be governed by the interaction between physics and biota. Furthermore, it is also assumed that studying in detail the effect of biota in fine sediment also processes will provide a better insight on water-bed exchange processes in the lake. The bed of the Markermeer consists of a clayey layer of historic deposits, stiff and not erodible under the prevailing hydrodynamics in the lake. On top of these parent deposits, a soft muddy layer is found. This mud has two distinct layers, an anoxic layer and an oxic layer. The oxic layer is located on top of the anoxic one, has a low bulk density and high organic matter content, and comes into resuspension frequently. The anoxic layer, located below the oxic one, has a higher bulk density and is resuspended occasionally. The first part of this thesis reviews the physical properties of the lake and of the sediments. The sediment properties are further studied through a number of field campaigns and laboratory measurements. This provides a characterization of the physical features affecting the fine sediment transport processes, in particular of the sediment characteristics. The results of this study reveal a detritus content of approximately 40% in the sediments. Sediments also contain Pyrite, which suggests important bacterial activity, which is in agreement with the observation of high detritus content. This bacterial activity is responsible for the reduction of sediments in absence of oxygen, and hence of the anoxic state of the sediments at the lower part of the muddy layer. Gradients in water content, thickness, organic matter content and chemical properties are found between the anoxic layer and the oxic layer. The size of the sediment particles in the oxic layer is slightly larger than the size of the sediments of the anoxic layer. This is likely caused by biological processes in the oxic layer, or by interaction with water-column biota upon re-suspension. Moreover, the sediments have a clay content of about 5 to 10%, which is enough for cohesive behavior of the bed. Some coarser sediments are present in the bed as well. These are mainly located in the north region of the lake, as revealed by the study of the spatial variability of the sediment properties. Next, the flocculation behavior of re-suspended sediments from the bed is investigated. Flocculation influences settling, and is therefore an important factor for the transport of fine sediments. In the Markermeer, sediment resuspended from the bed were found to flocculate, resulting in aggregates that vary in size as function of the turbulence level in the water column. Moreover, when sediments from the bed interact with the algae present in the water column, organic-inorganic flocs are formed. The properties of these combined flocs are determined by the type of algae present in the water column. In the case of the colonial blue-green algae Aphanothece, the organic-inorganic flocs attain larger sizes and flocculate faster than mineral flocs. When the filamentous blue-green algae Aphanizomenon are involved, the growth of the flocs may be limited by the filaments concentration in the suspension, resulting in smaller floc sizes. Thus, the type of algae in the water column also has an effect on the relationship between the total amount of suspended solids and the turbidity level, since, given the same amount of suspended sediments, smaller floc sizes will induce a higher turbidity. The erodability of the bed is also addressed in this thesis. Erosion is studied through a series of controlled laboratory experiments in an erosion microcosm. The results show that the erodability of the bed is strongly influenced by biological activity. The meiofauna in the muddy layer produces bioturbation, which is the main driver of the development of the easily re-suspended oxic layer. Without the effect of biota, thus in absence of the oxic layer, the erodability of the muddy layer on the bed would be much smaller, leading to resuspension only during storm events. Therefore, in the short term, bioturbation is responsible of the high turbidity in the lake. Another important finding regarding erodability, is that the parent clayey deposits of the bed become erodible only after bioturbation. However, bioturbation of the parent deposits is only possible when their surface is exposed to oxygen, activating the meiofauna on/in the sedimentary deposits. In the lake, 70% of the surface of the parent clayey deposits is currently covered by the anoxic muddy layer, and thus not reachable by oxygen. The lack of oxygen inhibits bioturbation, hence erosion of the parent deposits. Historical data reveals that the anoxic muddy layer was absent from the system before the lake’s closure from the IJsselmeer in the 70’s. Assuming that the muddy layer stems from erosion of the parent deposits after closure of the lake, the current cover of anoxic mud explains why the total amount of soft sediment in the Markermeer is still fairly limited, even though the current hydrodynamic conditions prevail already for more than four decades. The laboratory measurements of the erosion rate of the old deposits (upon bioturbation) suggest that the muddy layer may have been produced by erosion of the clayey old deposits in a period of about 10 to 15 years. Thus, bioturbation-driven erosion of the parent deposits is found to be the source of fine sediments within the system. With respect to sediment sinks, consolidation processes are analysed. The results show that consolidation occurs in lake Markermeer, constituting the main sink of fine sediments in the system. The consolidation process starts at a gelling concentration of approximately 60 g/l. The study of the first phase of consolidation, where permeability also plays a role, shows that a bed bioturbated by Tubifex has a higher permeability than an inorganic bed. This is attributed to the formation of tunnels and burrows within the sediment, which are produced by faunal activity. Finally, the effective stress, a measure of the strength of the bed at its final consolidation state, is found to be 20% smaller when fauna is present. This is likely related to the discontinuities that the activity of fauna create in the bed matrix. A one dimensional vertical modelling exercise is performed in the last part of the thesis, using the sand-mud bed module of Delft3D. The selected sediment transport parameters are obtained from the results of the laboratory measurements and experiments, as well as from the field measurements. The agreement between the model results and the observed suspended sediment concentrations at the lake is reasonably good, suggesting the validity of the measurements and of the modelling technique. Moreover, when the effect of biota is switched off in the model, the results are far off from the observations. This further supports the important influence of biota in the fine sediment dynamics in the lake. Overall, this work contributes to improve our understanding of water-bed exchange processes by introducing the effect of biota, which has been found to be a crucial factor for the fine sediment dynamics in the Markermeer. In the short term, the high turbidity present in the water column is directly linked with the biological activity on/in the bed. Furthermore, biota is crucial for the long term behaviour of sediments as well, as bioturbation of the old deposits constitutes the only source of sediments to the system. The latter is remarkable, since biota determines the long term sediment dynamics in the lake while acting in a very short time scale.