We present the computation of Lagrangian-based flow characterization measures for time-dependent, deformable-wall, finite-element blood flow simulations. Applicability of the algorithm is demonstrated in a fluid–structure interaction simulation of blood flow through a total cavopulmonary connection (Fontan procedure), and results are compared with a rigid-vessel simulation. Specifically, we report on several important Lagrangian-based measures including flow distributions, finite-time Lyapunov exponent fields, particle residence time, and exposure time calculations. Overall, strong similarity in Lagrangian measures of the flow between deformable and rigid-vessel models was observed. Copyright © 2012 John Wiley & Sons, Ltd.