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Two major lines of investigation have been pursued in this thesis: (1) More efficient, robust and realistic numerical techniques are designed for the simulation of complex turbulent fluid flows; (2) A new algorithm and its analysis is performed in the context of multiphasic fluid flow, for a cohesive fine-grained sediment (fluid mud) transport in estuaries. Estuaries exist between marine and freshwater system where waters of different physical, chemical and biological composition meet, combine and disperse primarily due to tidal influences. In the present thesis, the behavior of cohesive sediment in estuaries is reviewed based on the existing literature. Basic theories and recent developments are introduced to describe the formation of fluid mud from a very dilute suspension and its motion down a natural river bed with complex bathymetry. The present work contributes to the numerical simulation of complex turbulent multiphasic fluid flows encountered in estuarine channels, with the aim of the better understanding of the underlying physical processes as well as predicting realistically the cohesive sediment transport and bed morphology in such a zone. The model is based on the mass preserving method by using the so-called Raviart-Thomas finite element on the unstructured mesh in the horizontal plane. In the vertical, the computational domain is divided into number of layers at predefined heights and the method uses a conventional conforming P1 finite element scheme, with the advantage that the lowermost and uppermost layers variable height allow a faithful representation of the time-varying bed and free surface, respectively. Concerning the modeling of turbulence, the research effort focuses on the turbulence two-equation k - ε closure for the vertical parameterization of eddy viscosity. More precisely, a robust up-to-date algorithm is used for this issue. The new methodology is developed with the aim to account for more general relevant effects in the closure. The proposed model offers the capability to cope with the stiffness problem introduced by the large difference between the solid phase flow time scale and the hydrodynamic one, by using a sub-cycling strategy, whereas the splitting scheme is adopted with the aim of stability and the positivity of the relevant turbulent variables. The flexibility of the model and its performance are evaluated on several free-surface flow configurations with increasing complexity : homogeneous unsteady non-uniform flows in plane open channel flows, U-shaped (193°) curved open channel flow. Concerning the cohesive sediment transport, most of the existing models in the literature assume the analogous transport characteristics with that of the coarse sediment and adopt the relevant developed sediment transport for the latter to treat the former. Moreover, these existing models do not account for the consolidation of the mud-bed. The present research effort focused on a novel methodology based on the realistic empirical relationships, which accounts for the mutually exclusive processes for re-suspension and/or erosion and deposition of fine sediment, whereas only a limited range of bed shear stresses is allowed for simultaneous erosion and deposition to occur. Hence, on this basis, the new model investigated the bed morphology evolution by taking into account of the fluidization and/or consolidation of the fluid mud, which was handled by modeling the bed in three layers: (i) the mud-bed layer, (ii) the partially consolidated bed and (iii) the fully consolidated bed. The prediction of deposition/re-suspension using these two different methods lead to a non negligible difference in the results. Therefore, investigation of the true mechanism of erosion/deposition processes for cohesive sediments and their implementation in the numerical model is very important. This suggests that a realistic prediction must account for the fresh mud-bed re-suspension once deposited, as well as the consolidation and/or fluidization of the mud-bed deposits. Finally, the capability and improvements of the model are demonstrated, and its predicting performance is successfully evaluated by applying it to the simulation of the Po River Estuary (PRE) in Italy, which is the main source of river water discharge into the Northern Adriatic Sea. The analysis showed that the consolidation/fluidization process at the bed may have important influence on the prediction of bed morphology evolution. The three-layer approach used in this thesis is a first attempt to model these processes in detail within a numerical model.