The development of new efficient numerical techniques is a key point in computational fluid dynamics, and as a consequence in geological simulations. In this paper we present a model for simulating the dynamic of three-dimensional stratified sedimentary basins. This kind of problem contains several numerical complexities such as the presence of high viscosity jumps, or the necessity of tracking multiple surfaces of interface (horizons) independently. To overcome these difficulties, we introduce a new preconditioner, that reduces significantly the amount of time required to solve the finite element linear system resulting from the Stokes problem, and a new tracking method. Using a coupled level set–volume tracking method, indeed, an unlimited number of layers can be tracked with good mass conservation properties. Finally, to prove the efficiency of these new techniques we present the results and the computation performances obtained in simulations of a realistic case with four horizons, together with a complete description of the main physical quantities involved.