The boundary element method (BEM) is implemented for the simulation of three-dimensional transient flows of typical relevance to mixing. Creeping Newtonian and viscoelastic fluids of the Maxwell type are examined. A boundary-only formulation in the time domain is proposed for linear viscoelastic flows. Special emphasis is placed on cavity flows involving simple-and multiple-connected moving domains. The BEM becomes particularly suited in multiple-connected flows, where part of the boundary (stirrer or rotor) is moving, and the remaining outer part (cavity or barrel) is at rest. In this case, conventional methods, such as the finite element method (FEM), generally require remeshing or mesh refinement of the three-dimensional fluid volume as the flow evolves and the domain of computation changes with time. The BEM is shown to be much easier to implement since the kinematics of the elements bounding the fluid is known (imposed). It is found that, for simple cavity flow induced by a rotating vane at constant angular velocity, the tractions at the vane tip and cavity face exhibit non-linear periodic dynamical behavior with time for fluids obeying linear constitutive equations.