The main goal of this PhD thesis is to develop efficient Finite Element solvers for turbulent incompressible flows and turbulent magnetohydrodynamic (MHD) problems. In particular, the author studies the application of stabilized FEM to the simulation of turbulent flows and the efficient time integration techniques through Runge-Kutta schemes. All the research is done by developing FEMPAR, a massively parallel finite element software developed in LSSC group of CIMNE.