The research work reported in the present dissertation is aimed at the analysis of complex physical phenomena involving instabilities and nonlinearities occurring in fluids through state-of-the-art numerical modeling. Solutions of intricate fluid physics problems are devised in two particularly arduous situations: fluid domains with moving boundaries and the high-Reynolds-number regime dominated by nonlinear convective effects. Shear-driven flows of incompressible Newtonian fluids enclosed in cavities of varying geometries are thoroughly investigated in the two following frameworks: transition with a free surface and confined turbulence. The physical system we consider is made of an incompressible Newtonian fluid filling a bounded, or partially bounded cavity. A series of shear-driven flows are easily generated by setting in motion some part of the container boundary. These driven-cavity flows are not only technologically important, they are of great scientific interest because they display almost all physical fluid phenomena that can possibly occur in incompressible flows, and this in the simplest geometrical settings. Thus corner eddies, secondary flows, longitudinal vortices, complex three-dimensional patterns, chaotic particle motions, nonuniqueness, transition, and turbulence all occur naturally and can be studied in the same geometry. This facilitates the comparison of results from experiments, analysis, and computation over the whole range of Reynolds numbers. The flows under consideration are part of a larger class of confined flows driven by linear or angular momentum gradients. This dissertation reports a detailed study of a novel numerical method developed for the simulation of an unsteady free-surface flow in three-space-dimensions. This method relies on a moving-grid technique to solve the Navier-Stokes equations expressed in the arbitrary Lagrangian-Eulerian (ALE) kinematics and discretized by the spectral element method. A comprehensive analysis of the continuous and discretized formulations of the general problem in the ALE frame, with nonlinear, non-homogeneous and unsteady boundary conditions is presented. In this dissertation, we first consider in the internal turbulent flow of a fluid enclosed in a bounded cubical cavity driven by the constant translation of its lid. The solution of this flow relied on large-eddy simulations, which served to improve our physical understanding of this complex flow dynamics. Subsequently, a novel subgrid model based on approximate deconvolution methods coupled with a dynamic mixed scale model was devised. The large-eddy simulation of the lid-driven cubical cavity flow based on this novel subgrid model has shown improvements over traditional subgrid-viscosity type of models. Finally a new interpretation of approximate deconvolution models when used with implicit filtering as a way to approximate the projective grid filter was given. This led to the introduction of the grid filter models. Through the use of a newly-developed method of numerical simulation, in this dissertation we solve unsteady flows with a flat and moving free-surface in the transitional regime. These flows are the incompressible flow of a viscous fluid enclosed in a cylindrical container with an open top surface and driven by the steady rotation of the bottom wall. New flow states are investigated based on the fully three-dimensional solution of the Navier-Stokes equations for these free-surface cylindrical swirling flows, without resorting to any symmetry properties unlike all other results available in the literature. To our knowledge, this study delivers the most general available results for this free-surface problem due to its original mathematical treatment. This second part of the dissertation is a basic research task directed at increasing our understanding of the influence of the presence of a free surface on the intricate transitional flow dynamics of shear-driven flows.