In this work a general framework for the simulation of sedimentary basins in presence of salt structures is addressed. Sediments and evaporites are modeled as non-Newtonian fluids and the thermal effects induced by the presence of salt are taken into account. The computational strategy is based on a Lagrangian methodology with intensive grid adaptivity, together with a kinematic modeling of faults and different kinds of boundary conditions representing sedimentation, erosion, basement evolution, lithospheric compression and extension. The proposed methodology is applied to simple test cases as well as to a geological reconstruction of industrial interest.