Massively parallel finite element computations of 3D, unsteady incompressible flows, including those involving fluid-structure interactions, are presented. The computation with time-varying spatial domains are based on the deforming spatial domain/stabilized space-time (DSD/SST) finite element formulation. The capability to solve 3D problems involving fluid-structure interactions is demonstrated by investigating the dynamics of a flexible cantilevered pipe conveying fluid. Computations of flow past a stationary rectangular wing at Reynolds number 1000, 2500 and 107 reveal interesting flow patterns. In these computations, at each time step approximately 3 × 106 non-linear equations are solved to update the flow field. Also, preliminary results are presented for flow past a wing in flapping motion. In this case a specially designed mesh moving scheme is employed to eliminate the need for remeshing. All these computations are carried out on the Army High Performance Computing Research Center supercomputers CM-200 and CM-5, with major speed-ups compared with traditional supercomputers. The coupled equation systems arising from the finite element discretizations of these large-scale problems are solved iteratively with diagonal preconditioners. In some cases, to reduce the memory requirements even further, these iterations are carried out with a matrix-free strategy. The finite element formulations and their parallel implementations assume unstructured meshes.